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lambda
|
public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
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2024-08-26 |
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perl-parallel-forkmanager
|
public |
A simple parallel processing fork manager
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2024-08-26 |
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adapterremoval
|
public |
The AdapterRemoval v2 tool for merging and clipping reads.
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2024-08-25 |
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hmmer
|
public |
Biosequence analysis using profile hidden Markov models
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2024-08-24 |
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gxformat2
|
public |
Galaxy Workflow Format 2 Descriptions
|
2024-08-23 |
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bpipe
|
public |
Bpipe - a tool for running and managing bioinformatics pipelines
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2024-08-23 |
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art
|
public |
No Summary
|
2024-08-22 |
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pyseer
|
public |
Sequence Element Enrichment Analysis (SEER), python implementation
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2024-08-22 |
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whatshap
|
public |
phase genomic variants using DNA sequencing reads (haplotype assembly)
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2024-08-21 |
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python-hyphy-python
|
public |
HyPhy package interface library
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2024-08-21 |
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cyvcf2
|
public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
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2024-08-21 |
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bowtie2
|
public |
A fast and sensitive gapped read aligner.
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2024-08-21 |
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cutadapt
|
public |
Trim adapters from high-throughput sequencing reads
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2024-08-20 |
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muscle
|
public |
MUSCLE: multiple sequence alignment with high accuracy and high throughput
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2024-08-20 |
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r-sigqc
|
public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
|
2024-08-19 |
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pipits
|
public |
PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform
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2024-08-19 |
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htsbox
|
public |
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files.
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2024-08-16 |
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pasta
|
public |
An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm
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2024-08-15 |
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unicycler
|
public |
Hybrid assembly pipeline for bacterial genomes
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2024-08-14 |
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dsk
|
public |
DSK is a k-mer counter for reads or genomes.
|
2024-08-14 |
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discosnp
|
public |
reference-free small variant caller for short read sequencing data
|
2024-08-14 |
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lastz
|
public |
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
|
2024-08-13 |
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spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2024-08-13 |
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hyphy
|
public |
An open-source software package for comparative sequence analysis using stochastic evolutionary models.
|
2024-08-13 |
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solvebio
|
public |
The SolveBio Python client
|
2024-08-12 |
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rapidnj
|
public |
RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.
|
2024-08-12 |
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pkiss
|
public |
RNA secondary structure prediction including K-type and kissing hairpin- pseudoknots.
|
2024-08-11 |
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treetime
|
public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
|
2024-08-11 |
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poppunk
|
public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
|
2024-08-10 |
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pyani
|
public |
pyani provides a package and script for calculation of genome-scale average nucleotide identity.
|
2024-08-09 |
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nanoplot
|
public |
Plotting suite for long read sequencing data and alignments
|
2024-08-09 |
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comet-ms
|
public |
Comet is a command line tool that does MS/MS database search.
|
2024-08-09 |
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fastme
|
public |
a comprehensive, accurate and fast distance-based phylogeny inference program.
|
2024-08-09 |
|
rust-ncbitaxonomy
|
public |
A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering.
|
2024-08-09 |
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parafly
|
public |
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
|
2024-08-09 |
|
cgpbigwig
|
public |
BigWig manpulation tools using libBigWig and htslib
|
2024-08-08 |
|
picrust2
|
public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
|
2024-08-08 |
|
fwdpy11
|
public |
Forward-time population genetic simulation in Python.
|
2024-08-08 |
|
sonicparanoid
|
public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
|
2024-08-07 |
|
blast
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
|
2024-08-06 |
|
chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2024-08-06 |
|
perl-term-table
|
public |
Format a header and rows into a table
|
2024-08-06 |
|
irfinder
|
public |
Intron Retention Finder
|
2024-08-06 |
|
fastool
|
public |
A simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them.
|
2024-08-06 |
|
pyfaidx
|
public |
pyfaidx: efficient pythonic random access to fasta subsequences
|
2024-08-05 |
|
umi_tools
|
public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
|
2024-08-05 |
|
bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2024-08-05 |
|
trinity
|
public |
Trinity assembles transcript sequences from Illumina RNA-Seq data.
|
2024-08-04 |
|
iqtree
|
public |
Efficient phylogenomic software by maximum likelihood.
|
2024-08-04 |
|
tantan
|
public |
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
|
2024-08-02 |
