Search results

• MEGA
  Software suite for analyzing DNA and protein sequence data from species and populations.
  3 KB (337 words) - 20:30, 15 December 2020
• PolyGembler
  ...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
  3 KB (344 words) - 13:45, 3 November 2020
• P53MH
  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
  3 KB (344 words) - 18:35, 10 June 2022
• RNAstructure
  than single sequence secondary structure prediction. Finally, RNAstructure
  3 KB (359 words) - 21:58, 21 August 2022
• Ensembl Tools
  Ensembl Tools provide a number of ready-made tools for processing sequence data.
  3 KB (333 words) - 18:52, 12 August 2022
• Meraculous
  ...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
  3 KB (354 words) - 18:36, 10 June 2022
• Trinotate
  ...enced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt/Uniref90), protein domain identification (HMMER/PFAM
  3 KB (344 words) - 20:29, 7 December 2023
• TreeTime
  reeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree w
  3 KB (370 words) - 17:44, 2 November 2020
• ABruijn
  ...draft assembly by concatenating different parts of raw reads. This coarse sequence is then polished into a high quality assembly.
  3 KB (354 words) - 20:09, 24 August 2022
• MasHmap
  ...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
  3 KB (359 words) - 17:28, 27 May 2022
• Mobsuite
  Robertson, James et al. “Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidem
  3 KB (340 words) - 20:03, 10 October 2022
• Nanocaller
  ...to generate indel calling, and then creates consensus sequences for indel sequence prediction.
  3 KB (351 words) - 15:41, 16 March 2023
• Picard-tools
  ...nce Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.
  6 KB (882 words) - 15:25, 27 January 2023
• MentaLiST
  MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for
  3 KB (368 words) - 18:51, 10 June 2022
• AdapterRemoval
  AdapterRemoval may be used to recover a consensus adapter sequence for
  3 KB (357 words) - 20:47, 11 August 2022
• BinPacker
  ...sta format. Briefly, it works in two step: first, BinPacker partitions the sequence data into many individual splicing graphs, each capturing the full transcri
  3 KB (365 words) - 12:53, 15 August 2022
• Blast Job Scripts
  faSplit sequence ../large.fasta 120 blast_query_
  2 KB (358 words) - 20:27, 3 June 2022
• Musket
  ...: " Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data". Bioinformatics, 2013, 29(3): 308-315]
  3 KB (351 words) - 13:44, 19 August 2022
• Chewbbaca
  ...for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on
  3 KB (346 words) - 15:58, 20 October 2023
• PHYling
  analyses and also projected into coding sequence alignments for codon-based
  3 KB (375 words) - 18:17, 3 June 2022
• PASTA
  ...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
  3 KB (381 words) - 19:31, 24 August 2022
• NewTargets
  Bioinformatic sequence recovery for universal target-capture bait kits can be substantially improv
  3 KB (379 words) - 20:06, 12 August 2022
• VirusDetect
  ...tigs are provided as guidance to discovery novel viruses which do not show sequence similarity with known viruses.
  3 KB (377 words) - 23:22, 30 July 2020
• TransDecoder
  A minimum length open reading frame (ORF) is found in a transcript sequence
  3 KB (371 words) - 16:54, 22 August 2022
• Blast2GO
  the XML belonging to each sequence (provided in FASTA format). The program query sequence. Additionally you can add domain/motif based GO term obtained
  6 KB (920 words) - 14:08, 16 March 2023
• ATRAM
  * aTRAM.pl: this script runs aTRAM with a target sequence and the formatted short-read archive.
  3 KB (350 words) - 15:23, 12 August 2022
• SNAP
  [https://arxiv.org/abs/1111.5572 Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Arm
  3 KB (372 words) - 20:42, 12 August 2022
• Annocript
  ...putative long non-coding RNAs by using an heuristic based on homology and sequence features.
  3 KB (387 words) - 21:18, 6 December 2019
• Vcontact
  ...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
  3 KB (358 words) - 20:04, 27 May 2022
• Bracken
  ...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
  3 KB (402 words) - 19:01, 10 June 2022
• DAWGPAWS
  ...a Distributed Annotation Working Group (DAWG) in the annotation of genomic sequence contigs. These programs generate the multiple tracks of annotation evidence
  3 KB (381 words) - 21:20, 6 December 2019
• Metacrast
  ...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
  3 KB (392 words) - 17:58, 27 May 2022
• PerM
  The reference sequence(s) can be whole genomes with multiple chromosomes, the transcriptome or eve
  3 KB (396 words) - 17:40, 21 August 2022
• Glimmer
  ...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
  3 KB (391 words) - 17:09, 15 August 2022
• Giraf
  ...ational tool for identification of reassortments in influenza viruses from sequence databases of isolates. Reassortments in influenza - a process where strains
  3 KB (382 words) - 21:12, 7 December 2022
• MitoPhAST
  3) Reports various mitochondrial genes and sequence information in a simple table format.
  3 KB (382 words) - 14:27, 23 April 2020
• Saffrontree
  ...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
  3 KB (400 words) - 17:17, 31 May 2022
• Vcflib
  vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both:
  3 KB (390 words) - 20:54, 12 August 2022
• Liftoff
  ...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
  3 KB (399 words) - 13:14, 23 September 2020
• HaMStR
  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.
  3 KB (420 words) - 20:09, 12 August 2022
• AntiSMASH
  ...es. antiSMASH not only detects the gene clusters, but also offers detailed sequence analysis.
  3 KB (409 words) - 21:11, 6 December 2019
• CNCI
  ...tao Yu, Changhai Zhang, Yuanning Liu, RunSheng Chen and Yi Zhao* Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transc
  3 KB (374 words) - 14:09, 23 April 2021
• MACS
  ...mic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably
  3 KB (384 words) - 19:47, 12 August 2022
• GARLI
  ...rms phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. Version 2.
  3 KB (485 words) - 16:53, 15 August 2022
• Blast
  ...between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can
  3 KB (402 words) - 18:17, 12 August 2022
• V-Phaser
  ...to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) betw
  3 KB (390 words) - 20:07, 27 May 2022
• RepeatAnalysisTools
  sequence data generated with the PacBio No-Amp Targeted Sequencing
  4 KB (430 words) - 16:55, 15 December 2022
• Graphtyper
  ...n acyclic graph structure (a "pangenome reference"), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs,
  3 KB (373 words) - 15:43, 17 November 2021
• Coevol
  simultaneously on a sequence alignment, a matrix of quantitative characters
  3 KB (399 words) - 18:37, 12 August 2022
• Csubst
  * Simulated sequence evolution under specified scenarios of convergent evolution
  3 KB (380 words) - 22:12, 26 July 2023
• BMGE
  ...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
  3 KB (407 words) - 13:04, 15 August 2022
• Rascaf
  ...lter the connections by searching the merged gene sequences against public sequence databases. Finally, Rascaf uses these connections to select and/or re-arran
  3 KB (415 words) - 21:30, 21 August 2022
• MUMmer
  ...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
  3 KB (393 words) - 13:39, 19 August 2022
• AI Education and Training
  * Sequence Models
  3 KB (463 words) - 21:43, 7 November 2022
• TRNAscan-Se
  ...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
  3 KB (389 words) - 20:53, 12 August 2022
• VirusFinder
  ...ly developed algorithm, Virus intEgration site detection through Reference SEquence customization (VERSE) (manuscript in consideration) as well as other new fe
  3 KB (410 words) - 21:29, 6 December 2019
• Illumiprocessor
  trimmer for Illumina Sequence Data. Bioinformatics.
  4 KB (452 words) - 18:44, 15 August 2022
• Mauve
  ...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
  3 KB (448 words) - 19:49, 12 August 2022
• ARC
  ...es to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by
  3 KB (430 words) - 14:32, 12 August 2022
• SNPGenie
  ...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
  3 KB (423 words) - 18:41, 1 June 2022
• BALi-Phy
  BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single a
  3 KB (402 words) - 17:19, 14 December 2022
• BamBam
  ...ordinates in a BAM file as if it had been built from a different reference sequence
  3 KB (456 words) - 18:00, 12 August 2022
• Platon
  ...acterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial Genomics, 95, 295. https://do
  4 KB (437 words) - 17:14, 14 December 2022
• GSNP
  ...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
  3 KB (459 words) - 17:27, 15 August 2022
• Velvet
  Sequence assembler for very short reads.
  4 KB (523 words) - 17:06, 14 December 2022
• Ea-utils
  :: Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set o
  4 KB (438 words) - 14:54, 15 August 2022
• Amrfinderplus
  ...her classes of genes using protein annotations and/or assembled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data a
  4 KB (447 words) - 15:59, 27 May 2022
• Kmerfreq
  kmerfreq count K-mer (with size K) frequency from the input sequence data,typically sequencing reads data, and reference genome data is also app
  3 KB (449 words) - 19:28, 12 August 2022
• Sickle
  ...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
  4 KB (551 words) - 22:56, 21 August 2022
• Kraken
  ...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
  4 KB (483 words) - 19:28, 12 August 2022
• Stacks
  ...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
  4 KB (658 words) - 21:20, 2 January 2023
• Trinity
  ...entially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcrip
  4 KB (556 words) - 17:10, 22 August 2022
• GATK
  ...two packages. Our SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index calling) is a particular area of focus, and have b
  4 KB (540 words) - 16:53, 15 August 2022
• Khmer
  : Crusoe et al., The khmer software package: enabling efficient sequence analysis. 2014. doi: 10.6084/m9.figshare.979190
  4 KB (504 words) - 17:01, 14 December 2022
• ANNOVAR
  * Other functionalities: Retrieve the nucleotide sequence in any user-specific genomic positions in batch, identify a candidate gene
  4 KB (545 words) - 14:16, 12 August 2022
• DDT
  ...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:
  5 KB (754 words) - 19:24, 30 October 2023
• Transfer Data with Globus
  To transfer from a remote site to UFRC reverse the sequence in scenarios 2 and 3.
  10 KB (1,541 words) - 20:03, 17 January 2023

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