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parallel
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public |
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
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2023-09-22 |
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hmmer
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public |
Biosequence analysis using profile hidden Markov models
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2023-09-15 |
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modbam2bed
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public |
Summarise BAM files containing modified-base information to bedMethyl format.
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2023-08-31 |
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bwa
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public |
The BWA read mapper.
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2023-08-22 |
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csvtk
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public |
A cross-platform, efficient, practical CSV/TSV toolkit
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2023-08-21 |
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porechop
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public |
Adapter removal and demultiplexing of Oxford Nanopore reads
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2023-08-17 |
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ncls
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public |
Fast overlap datastructure.
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2023-08-17 |
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bioconductor-zlibbioc
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public |
An R packaged zlib-1.2.5
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2023-08-11 |
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bioconductor-rhdf5filters
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public |
HDF5 Compression Filters
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2023-08-10 |
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bioconductor-rhdf5lib
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public |
hdf5 library as an R package
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2023-08-10 |
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mash
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public |
Fast sequence distance estimator that uses MinHash
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2023-08-07 |
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capnproto-nossl
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public |
An insanely fast data interchange format and capability-based RPC system.
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2023-08-07 |
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r-phangorn
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public |
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
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2023-08-07 |
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r-fastmatch
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public |
Package providing a fast match() replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match() function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.
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2023-08-07 |
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r-igraph
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public |
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
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2023-08-07 |
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muscle
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public |
MUSCLE: multiple sequence alignment with high accuracy and high throughput
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2023-08-07 |
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r-ape
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public |
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
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2023-08-04 |
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racon
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public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
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2023-08-03 |
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miniasm
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public |
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
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2023-08-03 |
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mafft
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public |
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
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2023-08-03 |
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spoa
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public |
SIMD partial order alignment tool/library
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2023-08-03 |
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bedtools
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public |
A powerful toolset for genome arithmetic
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2023-08-03 |
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capnproto
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public |
An insanely fast data interchange format and capability-based RPC system.
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2023-08-02 |
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trnascan-se
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public |
tRNA detection in large-scale genomic sequences
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2023-08-02 |
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infernal
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public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
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2023-08-02 |
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diamond
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public |
Accelerated BLAST compatible local sequence aligner
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2023-08-02 |
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rasusa
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public |
Randomly subsample sequencing reads to a specified coverage
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2023-06-18 |
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mbtools
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public |
mbtools - toolkit for working with modification BAM files
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2023-06-18 |
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entrez-direct
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public |
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
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2023-06-18 |
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taxonkit
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public |
A Cross-platform and Efficient NCBI Taxonomy Toolkit
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2023-06-18 |
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bracken
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public |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
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2023-06-18 |
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kraken2
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public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2023-06-18 |
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sigfig
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public |
Python library for rounding numbers (with expected results)
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2023-06-18 |
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stringtie
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public |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
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2023-06-18 |
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gffcompare
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public |
GffCompare by Geo Pertea
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2023-06-18 |
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flye
|
public |
Fast and accurate de novo assembler for single molecule sequencing reads
|
2023-06-18 |
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seqkit
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public |
a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
|
2023-06-18 |
