Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

spack.io maintainers: snehring

py-hmmlearn 0.3.0
hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models.
1 version - Latest release: 6 months ago - 1 dependent package - 2,838 stars on GitHub - 1 maintainer
libbigwig 0.4.7
A C library for reading/parsing local and remote bigWig and bigBed files.
1 version - Latest release: over 1 year ago - 1 dependent package - 61 stars on GitHub - 1 maintainer
py-toytree 2.0.1
A minimalist tree manipulation and plotting library for use inside jupyter notebooks. Toytree com...
1 version - Latest release: 12 months ago - 1 maintainer
libidn 1.28
GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA 2003 specifi...
4 versions - Latest release: 3 months ago - 1 maintainer
modeltest-ng 0.1.7
Best-fit model selection
1 version - Latest release: about 2 years ago - 1 dependent package - 63 stars on GitHub - 1 maintainer
gcta 1.91.2beta
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of p...
2 versions - Latest release: about 2 years ago - 38 stars on GitHub - 1 maintainer
demuxlet
Genetic multiplexing of barcoded single cell RNA-seq
Latest release: 8 days ago - 94 stars on GitHub - 1 maintainer
Top 7.7% on spack.io
vsearch 2.22.1
VSEARCH is a versatile open-source tool for metagenomics.
4 versions - Latest release: over 1 year ago - 5 dependent packages - 556 stars on GitHub - 1 maintainer
py-itolapi 4.1.2
API for interacting with itol.embl.de
1 version - Latest release: 12 months ago - 1 dependent package - 1 maintainer
soapdenovo-trans 1.0.5
SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt t...
2 versions - Latest release: almost 2 years ago - 28 stars on GitHub - 1 maintainer
igv 2.16.2
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive ex...
3 versions - Latest release: 4 months ago - 1 maintainer
sepp 4.5.1
SEPP stands for SATe-enabled phylogenetic placement
1 version - Latest release: over 1 year ago - 68 stars on GitHub - 1 maintainer
javafx 20.0.1
JavaFX allows you to create Java applications with a modern, hardware- accelerated user interface...
1 version - Latest release: 8 months ago - 1 dependent package - 1 maintainer
subread 2.0.6
The Subread software package is a tool kit for processing next-gen sequencing data.
8 versions - Latest release: 10 months ago - 2 dependent packages - 1 maintainer
orca 5.0.3
An ab initio, DFT and semiempirical SCF-MO package Note: Orca is licensed software. You will need...
5 versions - Latest release: over 1 year ago - 1 maintainer
beagle 5.4
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
4 versions - Latest release: almost 2 years ago - 1 maintainer
Top 7.1% on spack.io
ncbi-rmblastn 2.14.0
RMBlast search engine for NCBI
3 versions - Latest release: 10 months ago - 3 dependent packages - 1 maintainer
aperture-photometry 3.0.2
Aperture Photometry Tool APT is software for astronomical research
3 versions - Latest release: 10 months ago - 1 maintainer
tecio 2022R2
The TecIO library allows third-party applications to read and write Tecplot file format.
1 version - Latest release: 9 months ago - 1 maintainer
bpp-popgen 2.4.1
The Bio++ Population Genetics Library
1 version - Latest release: almost 2 years ago - 1 dependent package - 1 maintainer
Top 5.8% on spack.io
diamond 2.1.7
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performa...
17 versions - Latest release: 10 months ago - 4 dependent packages - 1 maintainer
satsuma2 2016-11-22
Satsuma2 is an optimsed version of Satsuma, a tool to reliably align large and complex DNA sequen...
2 versions - Latest release: about 2 years ago - 31 stars on GitHub - 1 maintainer
prism 4.7
PRISM is a probabilistic model checker, a tool for formal modelling and analysis of systems that ...
2 versions - Latest release: 10 months ago - 1 maintainer
tmscore 20220227
TM-score is a metric for assessing the topological similarity of protein structures.
1 version - Latest release: 8 months ago - 1 maintainer
spectra 1.0.1
Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ lib...
3 versions - Latest release: almost 2 years ago - 1 maintainer
wise2 2.4.1
The Wise2 package is now a rather stately bioinformatics package that has be around for a while. ...
1 version - Latest release: 7 months ago - 1 maintainer
beast2 2.7.4
BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is...
6 versions - Latest release: 10 months ago - 1 maintainer
last 869
LAST finds similar regions between sequences, and aligns them. It is designed for comparing large...
1 version - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
emblmygff3 2.1
EMBLmyGFF3 converts an assembly in FASTA format along with associated annotation in GFF3 format ...
2 versions - Latest release: 8 months ago - 57 stars on GitHub - 1 maintainer
generax
GeneRax is a parallel tool for species tree-aware maximum likelihood based gene family tree infer...
Latest release: 12 days ago - 1 maintainer
Top 7.1% on spack.io
gmap-gsnap 2023-07-20
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Shor...
14 versions - Latest release: 7 months ago - 3 dependent packages - 1 maintainer
phylip 3.697
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evol...
1 version - Latest release: about 2 years ago - 1 dependent package - 1 maintainer
perl-text-nsp 1.29
The Ngram Statistics Package (NSP) is a suite of programs that aids in analyzing Ngrams in text ...
2 versions - Latest release: 8 months ago - 1 maintainer
tmalign 20220412
TM-align is an algorithm for sequence-order independent protein structure comparisons.
2 versions - Latest release: 10 months ago - 1 dependent package - 1 maintainer
snap-berkeley 2.0.3
SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths ...
4 versions - Latest release: 10 months ago - 1 dependent package - 1 maintainer
perl-devel-size 0.82_51
Devel::Size - Perl extension for finding the memory usage of Perl variables
2 versions - Latest release: 8 months ago - 1 dependent package - 1 maintainer
interproscan 5.63-95.0
InterProScan is the software package that allows sequences (protein and nucleic) to be scanned ag...
6 versions - Latest release: 6 months ago - 1 dependent package - 1 maintainer
Top 7.1% on spack.io
gatk 3.8.1
Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data
22 versions - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
ninja-phylogeny 0.98
NINJA is software for inferring large-scale neighbor-joining phylogenies.
1 version - Latest release: 8 months ago - 1 dependent package - 1 maintainer
montage 6.0
Montage is a toolkit for assembling Flexible Image Transport System (FITS) images into custom mos...
1 version - Latest release: about 2 years ago - 1 maintainer
Top 9.5% on spack.io
fasttree 2.1.11
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide...
2 versions - Latest release: over 1 year ago - 4 dependent packages - 1 maintainer
dock 6.9
DOCK is a molecular docking program used in drug discovery. This program, given a protein binding...
1 version - Latest release: about 2 years ago - 1 maintainer
metaeuk 6-a5d39d9
MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic...
1 version - Latest release: over 1 year ago - 1 maintainer
bamutil 1.0.15
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. ...
2 versions - Latest release: almost 2 years ago - 1 maintainer
usalign 20220829
US-align (Universal Structural alignment) is a unified protocol to compare 3D structures of diffe...
1 version - Latest release: 11 months ago - 1 maintainer
tassel 2017-07-22
TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage ...
1 version - Latest release: about 2 years ago - 1 maintainer
soapdenovo2 240
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the ...
2 versions - Latest release: about 2 years ago - 189 stars on GitHub - 1 maintainer
busco 4.1.3
Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orth...
3 versions - Latest release: about 2 years ago - 1 maintainer
Top 9.5% on spack.io
bpp-phyl 2.4.1
Bio++ phylogeny library.
2 versions - Latest release: almost 2 years ago - 2 dependent packages - 1 maintainer
mindthegap 2.0.2
MindTheGap is a software that performs integrated detection and assembly of genomic insertion var...
1 version - Latest release: about 2 years ago - 1 maintainer
methyldackel 0.6.1
MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILE...
1 version - Latest release: over 1 year ago - 126 stars on GitHub - 1 maintainer
perl-devel-checklib 1.16
Devel::CheckLib - check that a library is available
1 version - Latest release: 7 months ago - 1 dependent package - 1 maintainer
muscle5 5.1.0
MUSCLE is widely-used software for making multiple alignments of biological sequences.
1 version - Latest release: 12 months ago - 1 dependent package - 1 maintainer
salmon 1.10.2
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
7 versions - Latest release: 9 months ago - 1 dependent package - 1 maintainer
fastani 1.34
Fast, alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
2 versions - Latest release: 8 months ago - 2 dependent packages - 275 stars on GitHub - 1 maintainer
hapcut2 2017-07-10
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, des...
1 version - Latest release: about 2 years ago - 170 stars on GitHub - 1 maintainer
bpp-suite 2.4.1
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
2 versions - Latest release: almost 2 years ago - 1 dependent package - 1 maintainer
paml 4.10.7
PAML is a package of programs for phylogenetic analyses of DNA or protein sewuences using maximum...
4 versions - Latest release: 2 months ago - 1 dependent package - 1 maintainer
maq 0.7.1
Maq is a software that builds mapping assemblies from short reads generated by the next-generatio...
2 versions - Latest release: about 2 years ago - 1 maintainer
pbbam 2.1.0
The pbbam software package provides components to create, query, & edit PacBio BAM files and asso...
2 versions - Latest release: over 1 year ago - 2 dependent packages - 19 stars on GitHub - 1 maintainer
ea-utils 1.04.807
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter tri...
1 version - Latest release: about 2 years ago - 1 maintainer
pbmpi partition
A Bayesian software for phylogenetic reconstruction using mixture models
1 version - Latest release: about 2 years ago - 1 maintainer
Top 5.8% on spack.io
viennarna 2.6.4
The ViennaRNA Package consists of a C code library and several stand- alone programs for the pred...
4 versions - Latest release: 2 months ago - 4 dependent packages - 1 maintainer
esys-particle 3.0-alpha
ESyS-Particle is Open Source software for particle-based numerical modelling. The software implem...
1 version - Latest release: about 2 years ago - 1 maintainer
bucky 1.4.4
BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominan...
1 version - Latest release: about 2 years ago - 1 maintainer
repeatmodeler 2.0.4
RepeatModeler is a de-novo repeat family identification and modeling package.
2 versions - Latest release: 10 months ago - 1 maintainer
py-macs3 3.0.0b3
MACS: Model-based Analysis for ChIP-Seq
1 version - Latest release: 6 months ago - 645 stars on GitHub - 1 maintainer
Top 7.1% on spack.io
blat 37
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.
2 versions - Latest release: almost 2 years ago - 4 dependent packages - 1 maintainer
Top 4.9% on spack.io
bpp-core 2.4.1
Bio++ core library.
2 versions - Latest release: about 2 years ago - 5 dependent packages - 1 maintainer
Top 4.9% on spack.io
cdhit 4.8.1
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
2 versions - Latest release: about 2 years ago - 6 dependent packages - 1 maintainer
Top 5.8% on spack.io
usearch 11.0.667
USEARCH is a unique sequence analysis tool with thousands of users world-wide. Note: A manual dow...
2 versions - Latest release: almost 2 years ago - 5 dependent packages - 1 maintainer
Top 7.1% on spack.io
velvet 1.2.10
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.
1 version - Latest release: about 2 years ago - 3 dependent packages - 1 maintainer
Top 4.9% on spack.io
bpp-seq 2.4.1
Bio++ seq library.
2 versions - Latest release: about 2 years ago - 5 dependent packages - 1 maintainer
eagle 1.1.3
EAGLE: Explicit Alternative Genome Likelihood Evaluator
2 versions - Latest release: almost 2 years ago - 15 stars on GitHub - 1 maintainer
gemma 0.98.5
GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models...
1 version - Latest release: almost 2 years ago - 204 stars on GitHub - 2 maintainers
py-opentree 1.0.1
Library for interacting with Open Tree of Life resources.
1 version - Latest release: 12 months ago - 1 maintainer
ltr-retriever 2.9.4
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposo...
2 versions - Latest release: 10 months ago - 1 dependent package - 147 stars on GitHub - 1 maintainer
ldak 5.2
LDAK is a software package for analyzing GWAS data
2 versions - Latest release: 6 months ago - 1 maintainer
sentieon-genomics 202308.02
Sentieon provides complete solutions for secondary DNA analysis. Our software improves upon BWA, ...
9 versions - Latest release: 3 months ago - 1 maintainer
delly2 0.9.1
Delly2 is an integrated structural variant prediction method that can discover, genotype and visu...
2 versions - Latest release: about 2 years ago - 342 stars on GitHub - 1 maintainer
py-ete3 3.1.3
The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the re...
2 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
getorganelle 1.7.5.0
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
2 versions - Latest release: about 1 year ago - 191 stars on GitHub - 1 maintainer
dorado
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
Latest release: 20 days ago - 284 stars on GitHub - 1 maintainer
py-topiary-asr
Python framework for doing ancestral sequence reconstruction.
Latest release: 22 days ago - 1 maintainer
py-custom-inherit 2.4.1
A Python package that provides customized docstring inheritance schemes between derived classes a...
2 versions - Latest release: 12 months ago - 1 dependent package - 1 maintainer
shapemapper 2.2.0
ShapeMapper automates the calculation of RNA structure probing reactivities from mutational prof...
2 versions - Latest release: 3 months ago - 19 stars on GitHub - 1 maintainer
tbl2asn 2022-04-26
Tbl2asn is a command-line program that automates the creation of sequence records for submission ...
2 versions - Latest release: almost 2 years ago - 1 dependent package - 1 maintainer
pasta 1.8.3
PASTA (Practical Alignment using SATe and Transitivity)
1 version - Latest release: about 2 years ago - 1 dependent package - 74 stars on GitHub - 1 maintainer
py-cykhash 2.0.1
Cython wrapper for khash-sets/maps, efficient implementation of isin and unique.
1 version - Latest release: 6 months ago - 1 dependent package - 26 stars on GitHub - 1 maintainer
mothur 1.48.0
This project seeks to develop a single piece of open-source, expandable software to fill the bioi...
6 versions - Latest release: over 1 year ago - 242 stars on GitHub - 1 maintainer
py-pypng 0.20220715.0
PyPNG allows PNG image files to be read and written using pure Python.
2 versions - Latest release: 12 months ago - 1 dependent package - 1 maintainer
andi 0.14
andi is used for for estimating the evolutionary distance between closely related genomes.
2 versions - Latest release: about 2 years ago - 34 stars on GitHub - 1 maintainer
py-pastml 1.9.40
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
2 versions - Latest release: 12 months ago - 1 maintainer
py-toyplot 1.0.3
A modern plotting toolkit supporting electronic publishing and reproducibility.
2 versions - Latest release: 12 months ago - 1 dependent package - 1 maintainer
py-tesorter 1.4.6
TEsorter is coded for LTR_retriever to classify long terminal repeat retrotransposons (LTR-RTs) ...
1 version - Latest release: 8 months ago - 1 dependent package - 59 stars on GitHub - 1 maintainer