Search results

• UFCG
  * '''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.
  3 KB (431 words) - 17:41, 20 September 2023
• Uproc
  ...) 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
  3 KB (418 words) - 20:53, 12 August 2022
• SAMStat
  ...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
  3 KB (429 words) - 20:34, 12 August 2022
• Wengan
  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
  4 KB (472 words) - 20:55, 12 August 2022
• BEDTools
  #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
  3 KB (485 words) - 12:48, 15 August 2022
• TREEPUZZLE
  ...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
  4 KB (450 words) - 19:31, 10 June 2022
• Sate
  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
  7 KB (910 words) - 20:43, 21 December 2022
• BLAT
  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
  3 KB (484 words) - 13:03, 15 August 2022
• Fast-Plast
  ...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.
  4 KB (487 words) - 21:20, 6 December 2019
• Gffread
  GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
  2 KB (242 words) - 19:02, 12 August 2022
• SeCaPr
  A computational pipeline for processing Illumina sequence capture data
  2 KB (246 words) - 21:24, 6 December 2019
• InStruct
  ...subpopulations and classfies each individual into subpopulations given the sequence data.
  2 KB (254 words) - 18:00, 11 March 2020
• BppSuite
  BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
  2 KB (248 words) - 15:37, 9 December 2022
• Pyfasta
  Fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
  2 KB (238 words) - 19:58, 21 August 2022
• Randfold
  Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from
  2 KB (262 words) - 21:29, 21 August 2022
• Staden
  A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux
  2 KB (254 words) - 15:59, 22 August 2022
• Talesf
  ...sites for transcription activator-like (TAL) effectors in a given genomic sequence.
  2 KB (256 words) - 21:29, 6 December 2019
• Hgtector
  ...-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics.
  2 KB (253 words) - 17:04, 10 October 2022
• GeP
  Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates.
  2 KB (255 words) - 15:19, 10 June 2022
• LIGR
  LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of
  2 KB (249 words) - 19:55, 15 August 2022
• Metabin
  ...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
  4 KB (588 words) - 19:25, 18 August 2022
• Pysamstats
  ...utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
  2 KB (259 words) - 19:52, 29 September 2020
• PSMC
  This software package infers population size history from a diploid sequence
  2 KB (263 words) - 14:01, 28 February 2020
• CAMP
  CAMP is a sequence-based deep learning framework for multifaceted prediction of peptide-protei
  2 KB (255 words) - 18:00, 23 May 2022
• ParGenes
  ParGenes is a parallel tool that takes as input a set of multiple sequence alignments (typically from different genes) and infers their corresponding
  2 KB (265 words) - 13:31, 28 April 2021
• Odgi
  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
  2 KB (264 words) - 14:11, 15 July 2021
• Minced
  ...s) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.
  2 KB (263 words) - 15:38, 10 June 2022
• Scythe
  Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in pickin
  2 KB (262 words) - 20:36, 12 August 2022
• SMC++
  ...a program for estimating the size history of populations from whole genome sequence data.
  2 KB (268 words) - 23:52, 21 August 2022
• Automlsa2
  ...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.
  2 KB (266 words) - 15:25, 12 August 2022
• ProSplign
  Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm w
  2 KB (267 words) - 17:08, 1 June 2022
• Squigglenet
  ...ord Nanopore raw electrical signals as target or non-target for Read-Until sequence enrichment or depletion.
  2 KB (262 words) - 20:12, 9 May 2022
• Seqmagick
  We often have to convert sequence files between formats and do little manipulations on them, and it's not wor
  2 KB (269 words) - 22:35, 21 August 2022
• TrimAl
  ...ed removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
  2 KB (264 words) - 19:32, 24 August 2022
• MetaCherchant
  MetaCherchant is a tool for analysing genomic environment of a nucleotide sequence within a metagenome. The implementation is based on MetaFast source code.
  2 KB (269 words) - 21:22, 6 December 2019
• HmmCleaner
  ...to remove alignment and sequencing error containing segments from multiple sequence alignments (MSA) using profile hidden Markov models (pHMM). This tool is ba
  2 KB (275 words) - 22:25, 27 August 2020
• Graphaligner
  Rautiainen, M., Marschall, T. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 21, 253 (2020). https://doi.org/10.1186/s13
  2 KB (262 words) - 21:48, 12 January 2023
• EPACTS
  ...orm various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to
  2 KB (269 words) - 18:52, 12 August 2022
• FastQ-Screen
  ...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
  2 KB (274 words) - 16:05, 16 March 2020
• PyCogent
  PyCogent is a toolkit for making sense from sequence
  2 KB (275 words) - 17:20, 1 June 2022
• Trgt
  ...PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT c
  2 KB (273 words) - 14:45, 28 July 2023
• Megalodon
  ...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
  2 KB (271 words) - 22:24, 8 September 2020
• Trvz
  ...PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat.
  2 KB (273 words) - 14:46, 28 July 2023
• SInC
  ...tor for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
  2 KB (278 words) - 21:24, 6 December 2019
• DRAP
  ...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
  2 KB (280 words) - 21:20, 6 December 2019
• Exonerate
  * Exonerate is a generic tool for pairwise sequence comparison.
  2 KB (303 words) - 18:53, 12 August 2022
• OrthoFinder
  OrthoFinder is a program for identifying orthologous protein sequence families. It is written in python and runs as a single command that takes a
  2 KB (276 words) - 17:58, 19 August 2022
• M5nr
  The M5NR is an integration of many sequence databases into one single, searchable database (plus an index). A single si
  2 KB (286 words) - 19:46, 12 August 2022
• Pyani
  ...ticore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.
  2 KB (283 words) - 19:44, 21 August 2022
• GROCSVs
  ...tware pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural vari
  2 KB (274 words) - 21:21, 6 December 2019
• Pindel
  ...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
  2 KB (279 words) - 21:23, 6 December 2019
• ARKS
  Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. This project is a new
  2 KB (285 words) - 21:15, 6 December 2019
• IGV
  ...ts a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
  2 KB (276 words) - 18:42, 15 August 2022
• Srst2
  This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance
  2 KB (278 words) - 17:42, 13 December 2022
• SequelQC
  ...ram specifically for the PacBio Sequel platform that quickly processes raw sequence data from multiple SMRTcells producing multiple statistics and publication
  2 KB (280 words) - 21:24, 6 December 2019
• Clipkit
  ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. Steenwyk e
  2 KB (276 words) - 13:29, 15 August 2022
• PhaME
  ...SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses
  2 KB (287 words) - 14:18, 9 March 2020
• RepeatExplorer
  graph-based clustering analysis of sequence read similarities to identify
  2 KB (278 words) - 21:44, 21 August 2022
• Mashtree
  ...and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762]
  2 KB (280 words) - 13:30, 15 August 2022
• Gimmemotifs
  ...identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Pyt
  2 KB (293 words) - 15:41, 30 June 2023
• Cpc
  ...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
  2 KB (287 words) - 17:22, 9 June 2022
• RNAhybrid
  ...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
  2 KB (285 words) - 20:56, 12 August 2022
• CRISPResso2
  ...n of genome editing experiments. It aligns sequencing reads to a reference sequence, quantifies insertions, mutations and deletions to determine whether a read
  2 KB (282 words) - 13:25, 11 October 2022
• MPBoot
  ...program can reconstruct maximum parsimony trees for large DNA and protein sequence alignments. More importantly, it implements the method MPBoot for approxima
  3 KB (292 words) - 21:21, 6 December 2019
• AmPEPpy
  ...de sequences using the Distribution descriptor set from the Global Protein Sequence Descriptors. amPEPpy has improved portability, increased accuracy relative
  3 KB (291 words) - 14:13, 22 April 2021
• MEME
  * Search sequence databases using motifs.
  2 KB (292 words) - 19:50, 12 August 2022
• TraitRate
  rate of sequence evolution.
  2 KB (292 words) - 16:54, 22 August 2022
• InterProScan
  This interproscan software allows you to query your sequence against the InterPro databases.
  3 KB (334 words) - 19:23, 12 August 2022
• FastPlast
  ...roximately 30 minutes with no user mediation. In addition to a chloroplast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
  2 KB (288 words) - 20:23, 23 May 2022
• Haploflow
  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
  2 KB (287 words) - 20:31, 3 January 2022
• CViT
  ...Perl script used to quickly generate images that show features on genomic sequence. It is intentionally simplistic and low-tech; there are limitless possibili
  2 KB (294 words) - 12:09, 26 August 2022
• ZUMIS
  ...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,
  2 KB (302 words) - 17:55, 22 August 2022
• Medaka
  medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks
  2 KB (290 words) - 14:37, 21 August 2023
• SIFT
  ...rediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BL
  2 KB (303 words) - 20:40, 12 August 2022
• Kvarq
  ...rial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.
  2 KB (287 words) - 15:26, 21 June 2023
• BLASTDB
  ...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).
  7 KB (975 words) - 18:52, 10 April 2024
• Vamb
  Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance informatio
  3 KB (302 words) - 18:59, 1 February 2021
• Porechop
  ...hop performs thorough alignments to effectively find adapters, even at low sequence identity.
  2 KB (294 words) - 21:23, 6 December 2019
• GramCluster
  ...d accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
  2 KB (280 words) - 16:57, 10 June 2022
• PRINSEQ++
  ...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
  2 KB (298 words) - 18:11, 15 April 2020
• BPP
  ...ecies divergence times (tau), and for delimiting species using multi-locus sequence data from several closely related species.
  2 KB (294 words) - 18:21, 12 August 2022
• QTLtools
  ...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-
  2 KB (297 words) - 20:58, 21 August 2022
• Radorgminer
  The RADOrgMiner pipeline is designed to genotype sequence tags found in reduced genomic complexity libraries that originate from the
  3 KB (297 words) - 21:55, 6 July 2022
• Chimera
  maps, supramolecular assemblies, sequence alignments, docking results,
  3 KB (296 words) - 18:27, 12 August 2022
• MAFFT
  MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of mu
  2 KB (295 words) - 20:23, 15 August 2022
• StringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST) stringMLST is a tool for detecting the MLST of an isolate dir
  2 KB (292 words) - 20:45, 12 August 2022
• FastGEAR
  FastGEAR is a software for analyzing sequence alignments.
  3 KB (313 words) - 20:13, 18 October 2022
• FastUniq
  ...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
  3 KB (301 words) - 16:37, 15 August 2022
• Vg
  * paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks
  2 KB (299 words) - 14:42, 4 September 2020
• RepeatModeler
  ...ds for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout
  3 KB (297 words) - 20:32, 12 August 2022
• FAR
  ...s heuristic algorithm such as BLAST. Therefore the alignment of an adapter sequence to a read is very accurate.
  2 KB (298 words) - 18:54, 12 August 2022
• FastML
  ...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
  3 KB (312 words) - 18:54, 12 August 2022
• Wtdbg
  Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Techno
  3 KB (310 words) - 17:44, 22 August 2022
• GPhoCS
  ...om individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Paramete
  3 KB (300 words) - 21:20, 6 December 2019
• SortMeRNA
  SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core al
  3 KB (299 words) - 17:00, 10 June 2022
• ExpansionHunter
  ...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
  3 KB (335 words) - 20:36, 8 March 2022
• Physher
  ...ls to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology 14:163, 2014.]
  3 KB (312 words) - 15:28, 16 November 2021
• MIGRATE-N
  * 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)
  5 KB (636 words) - 16:05, 22 December 2022
• Pbmm2
  ...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
  3 KB (303 words) - 20:08, 31 May 2022
• MIRA
  MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger,
  2 KB (313 words) - 20:42, 18 August 2022

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