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perl-b-cow
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public |
B::COW additional B helpers to check COW status
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2025-03-25 |
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ncbi-amrfinderplus
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public |
AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
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2025-03-25 |
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pyrodigal
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public |
Python bindings to Prodigal, an ORF finder for microbial sequences.
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2025-03-25 |
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aragorn
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public |
ARAGORN, tRNA (and tmRNA) detection
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2025-03-25 |
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piler-cr
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public |
Identification and analysis of CRISPR repeats.
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2025-03-25 |
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clustalw
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public |
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
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2025-03-25 |
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paml
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public |
A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
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2025-03-25 |
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last
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public |
LAST finds & aligns related regions of sequences.
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2025-03-25 |
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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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2025-03-25 |
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hmmer
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public |
Biosequence analysis using profile hidden Markov models
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2025-03-25 |
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csvtk
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public |
A cross-platform, efficient, practical CSV/TSV toolkit
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2025-03-25 |
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porechop
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public |
Adapter removal and demultiplexing of Oxford Nanopore reads
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2025-03-25 |
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ncls
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public |
Fast overlap datastructure.
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2025-03-25 |
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bioconductor-zlibbioc
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public |
An R packaged zlib-1.2.5
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2025-03-25 |
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bioconductor-rhdf5filters
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public |
HDF5 Compression Filters
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2025-03-25 |
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bioconductor-rhdf5lib
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public |
hdf5 library as an R package
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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.
|
2025-03-25 |
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python-edlib
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public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
|
2025-03-25 |
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muscle
|
public |
MUSCLE: multiple sequence alignment with high accuracy and high throughput
|
2025-03-25 |
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parasail-python
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public |
Python bindings for the parasail C library containing implementations of pairwise sequence alignment algorithms.
|
2025-03-25 |
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racon
|
public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
|
2025-03-25 |
