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Biological sequence alignment tools and documentation

WebLogo is an application designed to make the generation of sequence logos as easy and painless as possible. ...precise description of, for example,a binding site, than would a consensus sequence.

Short Sequence Assembly software.

Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a

...robabilities. EvoLSTM brings modern machine-learning approaches to bear on sequence evolution. It will serve as a useful tool to study and simulate complex mut

...verlaps the end of the other). If seqfile2 is a database of sequences, the sequence in seqfile1 will be aligned with each of the sequences in seqfile2.

...e, that RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa.

...ts (alignment rows), which is different from the problem of poorly aligned sequence blocks (alignment columns) commonly addressed by alignment trimming softwar ...identification, visualization, and removal of outliers from large multiple sequence alignments. Journal of Open Source Software, 4(42), 1635, https://doi.org/1

...-hit produces a set of closely related protein families from a given fasta sequence database.

...orking with phylogenetic datasets. SuperCRUNCH can be run using any set of sequence data, as long as sequences are in fasta format with standard naming convent ...s (adjust sequence directions, adjust reading frames), several options for sequence alignment (Clustal-O, MAFFT, Muscle, MACSE), and multiple options for align

sequence as well as a modified version of the query sequence in which On average, almost 50% of a human genomic DNA sequence currently will

...graph constructor. It finds approximate locations of a query sequence in a sequence graph and incrementally augments an existing graph with long query subseque

...the resulting hits are written to stdout along with their position in the sequence, length, and a score determined by the length of the repeat and the number

...BioPerl FastA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm.

...next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. ...: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

...for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele. ...us, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, u

...ideally) match experimental PCR results. To enable searching of very large sequence databases (i.e. all of Genbank), ThermonucleotideBLAST can use run-time dat

seq_crumbs aims to be a collection of small sequence processing utilities. ...and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utili

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods

impg (Implicit Pangenome Graph) projects sequence ranges through many-way (e.g. all-vs-all) pairwise alignments built by tool ...htforward to use to extract FASTA sequences for downstream use in multiple sequence alignment (like mafft) or pangenome graph building (e.g., pggb or minigraph

...rence indexes built for the respective tools using the appropriate genomic sequence data. This page provides a short overview of our reference index building p ...most reference indexes to be built. In that case we'll use the non-masked sequence.

calling, sequence comparisons, and sequence assembly. Phred, Cross_match, Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the

...ion tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loa

...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer

...cal assembly of genomic regions matching a homologous query protein or DNA sequence. ...ssembler first collects the reads that can be locally aligned to the query sequence and assembles them into contigs. Additional reads are then found by alignin

Kalign is a fast multiple sequence alignment program for biological sequences. "Kalign 3: multiple sequence alignment of large data sets."

...tions, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output fil ...RCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude

...n in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer

This repo contains a set of neural transducer, e.g. sequence-to-sequence model, focusing on character-level tasks. It powers several papers and work

...rithm. Designed to efficiently detect all overlaps between noisy long-read sequence data. It efficiently estimates Jaccard similarity by compressing sequences

SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies. ...tez, B. Peng and S. M. Leal, Power analysis and sample size estimation for sequence-based association studies. Bioinformatics. (2014)]

...ches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX. GHOST-MP runs on a distributed memory system and proc

...of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer re

...t enrichment strategy. This workflow is suitable for Oxford Nanopore fastq sequence collections and requires a reference genome and a BED file of target coordi

T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine th T-Coffee: A novel method for multiple sequence alignments.

..., 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), t

...s for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well

...de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454

...tests, is a flexible software package for genetic association analysis for sequence datasets. ...ficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]

....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.

The Sequence Bloom Tree (SBT) is a method that will allow you to index a set of sequence. The code base provided here is an implementation of SBT written in

....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.

....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.

RS II sequencer. Generally speaking, this information is the sequence of all the reads to produce a highly accurate consensus sequence as the last step in the assembly

...ts, and outputs the phased haplotype blocks that can be assembled from the sequence reads.

Use it to find and download sequence, annotation, and metadata for genes and genomes Use '''datasets''' to download biological sequence data across all domains of life from NCBI.

Fairseq(-py) is a sequence modeling toolkit that allows researchers and developers to train custom mod A Fast, Extensible Toolkit for Sequence Modeling. Myle Ott and Sergey Edunov and Alexei Baevski and Angela Fan and

...improve the performance, both in runtime and quality for 454 and Illumina sequence reads.

....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions. F

...ing) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for L ...Soeding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics, doi: 10.1093/bioinformatics/bty1057 (2019).]

...e focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. There are many other packages which do this, probably the best known being

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced fr ...ne: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20]

...ackage for designing probe sets to use for nucleic acid capture of diverse sequence. of species. It allows blacklisting sequence from the design (e.g., background in microbial enrichment),

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configur ...med/21278185 Schmieder R and Edwards R: Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 2011, 6:e1728

...from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data.

...using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise com

...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. ...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLoS genetics, 13(1), p.e1006529.

Multiple sequence alignments may contain a variety of completely-specified characters. Here a for multiple sequence alignments. NAR Genomics and Bioinformatics 2 (2), lqaa024.

REPdenovo is designed for constructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides ...elsen and Yufeng Wu, REPdenovo: Inferring de novo repeat motifs from short sequence reads, PLoS One 11.3 (2016): e0150719.]

The Sequence Similarities by Markov Chain Monte Carlo (SeSiMCMC) algorithm careful Bayesian analysis to consider site absence in a sequence.

...and align the resulting contigs to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (<2GB RAM, ...novo assembly of all recruited reads, a set of contigs is generated. Only sequence contigs equal or larger than 200nt in length are considered for further ana

MAGUS is a tool for piecewise large-scale multiple sequence alignment. Original MAGUS paper: Smirnov, V. and Warnow, T., 2020. MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics. https://doi.org/10.1093/b

...d using the Illumina sequencing platform. In principle, it should work for sequence data from other sequencing platforms. The method requires each pool to be s

...nomic sequences. Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorg

...put sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-se

...more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.

...ude the portion of DNA sequence (as well as certain length of the flanking sequence – given by the user, default = 50 bp) matching subjects in a protein data

...r to search an optimal set of paths (transcripts) that can be supported by sequence data and could explain all observed splicing events of each locus.

* Handle big sequence data, e.g: * Use sequence quality data properly.

...terior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading generation and manipulation of multiple sequence alignments using

...w sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, i

...nction that selects how many position to consider for each of the multiple-sequence alignment.

...assemblies. JASPER is substantially faster than polishing methods based on sequence alignment, and more accurate than currently available k-mer based methods.

...BOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards

...most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more sensi

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of ...., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using T

Follow these steps to run Maq. All you need is a reference sequence file in the FASTA format. Prepare a reference sequence (ref.fasta), better a bacterial genome to make the test run faster.

ViralMSA is a tool to perform reference-guided multiple sequence alignment of viral genomes. ViralMSA wraps around existing read mapping too ...Moshiri N (2020). "ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. btaa743. doi:10.1093/bioinform

...alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for

...h some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's m ...suitable for both ends of paired-end libraries), but accepts other adapter sequence, too

...is a python package of tools and pipelines for working with ribosomal DNA sequence data generated with the PacBio(R) SMRT sequencing. rDnaTools works by wrapp ...al Ecology community, and their existing tools for analyzing ribosomal DNA sequence data. Since the core of the analyses wrapped by rDnaTools come from the Mot

...quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user ...n of microsatellite sequences from paired-end Illumina High-Throughput DNA sequence data (ver. 1.1, February 2014): U.S. Geological Survey Data Series 778.

..., which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.

...e data is encoded based on the information content at a particular aligned sequence site. This contextual encoding allows for rapid computation of phylogenetic

...write complex descriptors before starting a search. Instead ERPIN reads a sequence alignement and secondary structure, and automatically infers a statistical ...ert A. (2001) Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Biol. 313:1003-11]

...nce Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments

...ed on a comparison of their protein domain content, order, copy number and sequence identity.

PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to A fast computation approach to obtain pairwise sequence alignment scores enabled the generation of precomputed PROVEAN predictions

available genotype and shotgun sequence data to estimate unobserved Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Ep

...ragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy ...Michelle C. Stitzer. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.

...avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity e

...grates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings

INDELible is a new, portable, and flexible application for biological sequence simulation that combines many features in the same place for the first time ...tcher, W. and Yang, Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. and Evol. 2009 26(8):1879-1888]

...ikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikText converts alignments to different text-base

...sion by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, fo

* scrappie squiggle Create approximate squiggle for sequence * scrappie seqmappy Map signal to sequence via basecall posteriors

with the length of the target sequence. A rough guideline is 1 GB of memory for 1 Mb of input sequence.

...Repeats with pattern size in the range from 1 to 2000 bases are detected. Sequence information sent to the server is confidential and deleted after program ex

* EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors * PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles

* '''ufcg train''' generates sequence model of your own fungal marker gene, even from a small set of seed sequenc * '''ufcg align''' conducts multiple sequence alignment of the genes from the set of marker gene profiles.

...) toolbox implements a novel algorithm ("Mosaic Matching") for large-scale sequence analysis and is now available in terms of an open source C library. UProC i

...a reference genome in the alignment / map format (SAM/BAM). To monitor the sequence quality over time and to identify problems it is necessary to report variou SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM fil

alignments can be inferred by building paths on a sequence graph. To achieve this, Wengan builds a new sequence graph called the Synthetic Scaffolding Graph (SSG). The SSG is built from

#Calculating the depth and breadth of sequence coverage across defined "windows" in a genome. ...ntrol over how output is reported. Most recently, I have added support for sequence alignments in BAM ([http://samtools.sourceforge.net/]) format, as well as f

...t computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the d

SATé is a software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated .... Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation of sequence alignments and phylogenetic trees." Science, 324(5934), pp. 1561-1564, 19 J

sequence. BLAT is much faster than older tools such as BLAST for nucleotide and the genome likely to be similar to the query sequence. It performs an alignment

...roximately 30 minutes with no user mediation. In addition to a chloroplast sequence, Fast-Plast identifies chloroplast genes present in the final assembly. .... Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.

GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

A computational pipeline for processing Illumina sequence capture data

...subpopulations and classfies each individual into subpopulations given the sequence data.

BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

Fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.

Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux

...sites for transcription activator-like (TAL) effectors in a given genomic sequence.

...-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics.

Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates.

LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of

...for faster and more accurate taxonomic assignment of single and paired-end sequence reads of varying lengths (≥45 bp) obtained from both Sanger and next-gene ...g Blastx. The MetaBin web server allows users to upload their own data, as sequence reads or Blastx output, to carry out taxonomic analysis. It provides severa

...utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

This software package infers population size history from a diploid sequence

CAMP is a sequence-based deep learning framework for multifaceted prediction of peptide-protei

ParGenes is a parallel tool that takes as input a set of multiple sequence alignments (typically from different genes) and infers their corresponding

odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such gra

...s) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in pickin

...a program for estimating the size history of populations from whole genome sequence data.

...ips between genes and organisms. The general idea is to allow the input of sequence data along with marker genes and output a robust phylogenetic tree.

Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm w

...ord Nanopore raw electrical signals as target or non-target for Read-Until sequence enrichment or depletion.

We often have to convert sequence files between formats and do little manipulations on them, and it's not wor

...ed removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

MetaCherchant is a tool for analysing genomic environment of a nucleotide sequence within a metagenome. The implementation is based on MetaFast source code.

...to remove alignment and sequencing error containing segments from multiple sequence alignments (MSA) using profile hidden Markov models (pHMM). This tool is ba

Rautiainen, M., Marschall, T. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 21, 253 (2020). https://doi.org/10.1186/s13

...orm various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to

...lows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with wha

PyCogent is a toolkit for making sense from sequence

...PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT c

...is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich bas

...PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat.

...tor for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

...shed method to study transcription of organisms lacking a reference genome sequence. Available packages such as Trinity and Oases have proven to be able to hig

* Exonerate is a generic tool for pairwise sequence comparison.

OrthoFinder is a program for identifying orthologous protein sequence families. It is written in python and runs as a single command that takes a

The M5NR is an integration of many sequence databases into one single, searchable database (plus an index). A single si

...ticore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.

...tware pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural vari

...ons and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of thes

Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. This project is a new

...ts a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance

...ram specifically for the PacBio Sequel platform that quickly processes raw sequence data from multiple SMRTcells producing multiple statistics and publication

ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. Steenwyk e

...SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses

graph-based clustering analysis of sequence read similarities to identify

...and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762]

...identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Pyt

...Calculator distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts. Last version of CPC1 is widely used by w

...NA. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting part of the long one. The tool is primari

...n of genome editing experiments. It aligns sequencing reads to a reference sequence, quantifies insertions, mutations and deletions to determine whether a read

...program can reconstruct maximum parsimony trees for large DNA and protein sequence alignments. More importantly, it implements the method MPBoot for approxima

...de sequences using the Distribution descriptor set from the Global Protein Sequence Descriptors. amPEPpy has improved portability, increased accuracy relative

* Search sequence databases using motifs.

rate of sequence evolution.

This interproscan software allows you to query your sequence against the InterPro databases.

...roximately 30 minutes with no user mediation. In addition to a chloroplast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.

Haploflow is a strain-aware viral genome assembler for short read sequence data. It uses a flow algorithm on a deBruijn graph data structure to resolv

...Perl script used to quickly generate images that show features on genomic sequence. It is intentionally simplistic and low-tech; there are limitless possibili

...files. In the most common cases, you will have a read containing the cDNA sequence and other read(s) containing UMI and Cell Barcode information. Furthermore,

medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks

...rediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BL

...rial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.

...10.1 of the Rfam collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). ...lies) of the Rfam collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance informatio

...hop performs thorough alignments to effectively find adapters, even at low sequence identity.

...d accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.

...rogram. It can be used to filter, reformat or trim genomic and metagenomic sequence data. It is 5X faster than prinseq-lite.pl and uses less RAM thanks to the

...ecies divergence times (tau), and for delimiting species using multi-locus sequence data from several closely related species.

...set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-

The RADOrgMiner pipeline is designed to genotype sequence tags found in reduced genomic complexity libraries that originate from the

maps, supramolecular assemblies, sequence alignments, docking results,

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of mu

Fast k-mer based tool for multi locus sequence typing (MLST) stringMLST is a tool for detecting the MLST of an isolate dir

FastGEAR is a software for analyzing sequence alignments.

...as an ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format. FastUniq identifies duplicates by comparing sequence

* paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks

...ds for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout

...s heuristic algorithm such as BLAST. Therefore the alignment of an adapter sequence to a read is very accurate.

...together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. FastML is generic and is appli

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Techno

...om individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Paramete

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core al

...ber of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger t

...ls to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology 14:163, 2014.]

* Sequence data using Felsenstein's 84 model with or without site rate variation, * Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)

...en used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the offi

MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger,

*convert: Simple manipulation of DNA sequence data

CAP3 is a sequence assembly program.

...ure annotation and haplotype-resolved consensus computation using multiple sequence alignments.

Inputs to EVM include the genome sequence, gene predictions and alignment data in GFF3 format, and a list of numeric

Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.

...) are transcribed from LINE 1 antisense promoter and include the L1 5’UTR sequence in antisense orientation followed by the adjacent genomic region.

...tion and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final asse

IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary

...nism in support of high performance data downloads and submission. The raw sequence files, typically stored as BAM or FASTQ, make up the bulk of data. The size

...a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). F

...that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-S

...rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11).]

...ind the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

It accounts for sequence substitutions, gene duplication, gene loss and horizontal gene transfer.

...nd Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing ins

...ctures for the representation of de Bruijn graphs are important for genome sequence assembly. A fully dynamic data structure supporting efficient and exact mem

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is

...(2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30]

...nt paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned t

...origin of introns. GenePainter maps gene structures onto protein multiple sequence alignments. Gene structures, as provided by e.g. WebScipio, are aligned wit

*fastq-match : (smith-waterman) local sequence alignment

...em is to build a histogram of all substrings of length k in a given genome sequence. Gerbil is a k-mer counter that is specialized for high effiency when count

databases (publication, sequence, structure, gene, variation, expression, etc.)

...cing. Chemical modifications are recorded as noncomplementary nucleotides (sequence changes) during cDNA synthesis and are thus not significantly affected by w

DNA sequence reads, designed to just work with excellent speed and

by identifying local duplications within a sequence. Other programs provide

...s local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.

...ore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the bes

...am takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. Final assembly should be

...models. Pan-allele predictors supporting virtually any MHC allele of known sequence are available for testing (see below). MHCflurry runs on Python 2.7 and 3.4

...-level approach it is avoided to run a full model through an entire genome sequence allowing faster predictions.

ClonalFrame can be applied to any kind of sequence data, from a

...ed orthologous plant gene family clusters, and builds gene family multiple sequence alignments and their corresponding phylogenies.

...utomation. It can also do IT orchestration, where you have to run tasks in sequence and create a chain of events which must happen on several different servers

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries t

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of

...., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.]

Wgsim is a small tool for simulating sequence reads from a reference genome.

...want to know what is contained within your sample or how abundant a given sequence is relative to another.

...., Sun, H., Jiao, W. et al. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol 20, 277 (2019) doi:10

...ftware tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill

...a comprehensive QC report to tell if there is anything unusual about your sequence. Each test is flagged as a pass, warning or fail depending on how far it d

...D, Fostier J, Verachtert W (2019) elPrep 4: A multithreaded framework for sequence analysis. PLoS ONE 14(2): e0209523. https://doi.org/10.1371/journal.pone.02

substrings is a central step in many analyses of DNA sequence. JELLYFISH can

Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software captures summary information for resequenci

PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of met

...t of the commonly used (and computationally tractable) models of molecular sequence evolution.

...ences for multiple lines or multiple species is a cost-efficient method to sequence and analyze a broad range of data.

ClonalFrameML can be applied to any type of aligned sequence data, but is

...rithm uses a series of disk-backed sorts and passes over the alignment and sequence inputs to allow the graph to be constructed from very large inputs that are

Software suite for analyzing DNA and protein sequence data from species and populations.

...population, as well as high coverage (i.e. greater than 30X) whole genome sequence data on a reference sample, or alternatively the availability of a set of r

Computes a score between 0 and 100 for each site in the DNA sequence of a gene. A high score indicates an increased probability that n nucleotid

than single sequence secondary structure prediction. Finally, RNAstructure

Ensembl Tools provide a number of ready-made tools for processing sequence data.

...mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redunda

...enced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt/Uniref90), protein domain identification (HMMER/PFAM

reeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree w

...draft assembly by concatenating different parts of raw reads. This coarse sequence is then polished into a high quality assembly.

...nation of Minimizers and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is aut

Robertson, James et al. “Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidem

...to generate indel calling, and then creates consensus sequences for indel sequence prediction.

...nce Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for

AdapterRemoval may be used to recover a consensus adapter sequence for

...sta format. Briefly, it works in two step: first, BinPacker partitions the sequence data into many individual splicing graphs, each capturing the full transcri

faSplit sequence ../large.fasta 120 blast_query_

...: " Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data". Bioinformatics, 2013, 29(3): 308-315]

...for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on

analyses and also projected into coding sequence alignments for codon-based

...ng an iterative approach. In each iteration, it first estimates a multiple sequence alignment using the current tree as a guide and then estimates a ML tree on

Bioinformatic sequence recovery for universal target-capture bait kits can be substantially improv

...tigs are provided as guidance to discovery novel viruses which do not show sequence similarity with known viruses.

A minimum length open reading frame (ORF) is found in a transcript sequence

the XML belonging to each sequence (provided in FASTA format). The program query sequence. Additionally you can add domain/motif based GO term obtained

* aTRAM.pl: this script runs aTRAM with a target sequence and the formatted short-read archive.

[https://arxiv.org/abs/1111.5572 Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Arm

...putative long non-coding RNAs by using an heuristic based on homology and sequence features.

...ool to perform guilt-by-contig-association classification of viral genomic sequence data. It's designed to cluster and provide taxonomic context of viral metag

...the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine

...a Distributed Annotation Working Group (DAWG) in the annotation of genomic sequence contigs. These programs generate the multiple tracks of annotation evidence

...ttern search algorithm to rapidly select reads that contain an expected DR sequence. It then proceeds through reads identified in the previous step to find DR

The reference sequence(s) can be whole genomes with multiple chromosomes, the transcriptome or eve

...which we term an Interpolated Context Model or ICM). The models for coding sequence are 3-periodic nonhomogenous Markov models. Improvements made in version 3

...ational tool for identification of reassortments in influenza viruses from sequence databases of isolates. Reassortments in influenza - a process where strains

3) Reports various mitochondrial genes and sequence information in a simple table format.

...om raw reads or from assembled sequences, without the need for a reference sequence or de novo assemblies. SaffronTree takes FASTQ/FASTA files as input and use

vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both:

...es. For each gene, Liftoff finds the alignments of the exons that maximize sequence identity while preserving the transcript and gene structure. If two genes i

HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

...es. antiSMASH not only detects the gene clusters, but also offers detailed sequence analysis.

...tao Yu, Changhai Zhang, Yuanning Liu, RunSheng Chen and Yi Zhao* Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transc

...mic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably

...rms phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. Version 2.

...between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can

...to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) betw

sequence data generated with the PacBio No-Amp Targeted Sequencing

...n acyclic graph structure (a "pangenome reference"), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs,

simultaneously on a sequence alignment, a matrix of quantitative characters

* Simulated sequence evolution under specified scenarios of convergent evolution

...w-software-for-selection-of-phylogenetic-informative-regions-from-multiple-sequence-alignments/}} ...Gathering with Entropy), that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. For each character, B

...lter the connections by searching the merged gene sequences against public sequence databases. Finally, Rascaf uses these connections to select and/or re-arran

...ogram included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignm

* Sequence Models

...eed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. It applies our COVE soft

...ly developed algorithm, Virus intEgration site detection through Reference SEquence customization (VERSE) (manuscript in consideration) as well as other new fe

trimmer for Illumina Sequence Data. Bioinformatics.

...ources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in u

...es to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by

...ity of a virus population within a single host, it might be appropriate to sequence the pooled nucleic acid content of the virus in a blood sample from that ho

BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single a

...ordinates in a BAM file as if it had been built from a different reference sequence

...acterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial Genomics, 95, 295. https://do

...e of each base. These quality scores are used as the standard of consensus sequence calling. Combined with the prior probability of dbSNP allele, it gets a low

Sequence assembler for very short reads.

:: Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set o

...her classes of genes using protein annotations and/or assembled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data a

kmerfreq count K-mer (with size K) frequency from the input sequence data,typically sequencing reads data, and reference genome data is also app

...strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entir

...s by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to t

...s developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeogr

...entially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcrip

...two packages. Our SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index calling) is a particular area of focus, and have b

: Crusoe et al., The khmer software package: enabling efficient sequence analysis. 2014. doi: 10.6084/m9.figshare.979190

* Other functionalities: Retrieve the nucleotide sequence in any user-specific genomic positions in batch, identify a candidate gene

...u were going to submit it to the queue. Be sure that you add the following sequence before the <code>mpiexec</code> command in your script:

To transfer from a remote site to UFRC reverse the sequence in scenarios 2 and 3.