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sci-biology/fastp

An ultra-fast all-in-one FASTQ preprocessor

sci-biology/AlignGraph

Reference-genome-assisted asssembly of contigs/scaffolds using PE reads

sci-biology/BRANCH

Extend partial transcripts with sequence from other reads or genomic contigs

sci-biology/KaKs_Calculator

Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates

sci-biology/KING

Check family relationship and infer population structure

sci-biology/MuSeqBox

Parse and filter BLAST output into tab-delimited file

sci-biology/aghermann

A sleep-research experiment manager, EDF viewer & Process S simulator

sci-biology/bamql

Extract reads from BAM files

sci-biology/brat

Bisulfite-treated Reads Analysis Tool (short read mapper)

sci-biology/brat_bw

Bisulfite-aware short read mapper, FM-index, no InDel support

sci-biology/brat_nova

Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align

sci-biology/codonw

Multivariate statistical analysis of codon and amino acid usage

sci-biology/cnrun

A NeuroML-enabled, precise but slow neuronal network simulator

sci-biology/coral

Error corrector for Illumina and Roche/454 reads using multiple alignment info

sci-biology/edena

De novo short read OLC assembler (overlap-layout-consensus)

sci-biology/erpin

Easy RNA Profile IdentificatioN, an RNA motif search program

sci-biology/epga

De novo assembler using distribution of reads and insert size

sci-biology/exonerate-gff3

exonerate-2.2.0 with patches to add GFF3 formatted output

sci-biology/fsl

Analysis of functional, structural, and diffusion MRI brain imaging data

sci-biology/germline

Find shared segments of Identity by Descent (IBD) between pairs of individuals

sci-biology/grabix

Provide random access to text files BGZF compressed with bgzip

sci-biology/grappa

Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

sci-biology/hexamer

Predict CDS using 6mers without deriving information from base composition

sci-biology/idba

De novo De Bruijn graph assembler iteratively using multimple k-mers

sci-biology/karect

Error-correct mismatches and InDels of raw reads incl. paired-end

sci-biology/lastz

A pairwise DNA sequence aligner, a BLASTZ replacement

sci-biology/merlin

Statistical analysis of gene flow in pedigrees

sci-biology/mip-scaffolder

Scaffold contigs using ABI Solid or Illumina mate pair info

sci-biology/miranda

An algorithm for finding genomic targets for microRNAs

sci-biology/mreps

Identification of serial/tandem repeats in DNA sequences

sci-biology/msautil

Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)

sci-biology/mrfast

Micro Read Fast Alignment Search Tool

sci-biology/nextclip

Split Illumina Nextera long mate-pairs

sci-biology/nrcl

Containment clustering and layout utility for processing pairwise alignments

sci-biology/perga

Paired End Reads Guided Assembler

sci-biology/quicktree

Rapid reconstruction of phylogenies by the Neighbor-Joining method

sci-biology/proda

Multiple alignment of protein sequences with repeated and shuffled elements

sci-biology/rnaplex

RNA-RNA interaction search

sci-biology/psx

parallel multi-FASTA file processing tool from TIGR Gene Indices project tools

sci-biology/sabre

Barcode demultiplexing and trimming tool for Illumina FastQ files

sci-biology/sff_dump

Convert Roche SFF files to FASTA file format

sci-biology/snap

HMM-based prokaryotic and eukaryotic gene prediction tool

sci-biology/ssaha2-bin

SSAHA2: Sequence Search and Alignment by Hashing Algorithm

sci-biology/ugene

A free open-source cross-platform bioinformatics software

sci-biology/vt

A tool set for short variant discovery in genetic sequence data

sci-biology/yaha

DNA mapper for single-end reads to detect structural variants (SV)

sci-biology/zmsort

Merge-sort utility for compressed alignment files, with multi-file output

sci-biology/BRAKER

Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS

sci-biology/GAL

Genome Annotation Library (incl. fasta_tool)

sci-biology/BEP032tools

Conversion and validation tools for BEP 032