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orthofinder

Accurate inference of orthologous gene groups made easy.

Versions:2.1.2
License:GPL v3
Categories:bioinformatics
p4

P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.

Versions:201804
License:GPLv2
Categories:Bayesian, phylogenetics
p4vasp

This software is Open Source. p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP).

Versions:0.3.29
License:http://www.p4vasp.at
Categories:crystal symmetries, electronic structure, vizualization
p7zip

p7zip is a port of 7za.exe, compression app, for POSIX systems like Unix.

Versions:15.14.1
License:http://www.7-zip.org/license.txt
Categories:7zip, archiver, archives, compression, zip
paml

PAML (for Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood.

Versions:4.9d
License:UNKNOWN
Categories:bioinformatics
pandoc

Pandoc is open-source software, maintained by volunteers working in their free time. Please keep that in mind when asking for help.

Versions:2.4
License:GPL
Categories:Markup Language Tool
parallel

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

Versions:20171222; 20161022
License:GPLv3
Categories:bioinformatics
parallel-fastq-dump

parallel fastq-dump wrapper

Versions:0.6.5
License:GPLv2
Categories:bioinformatics
paraver

Expressive powerful and flexible trace visualizer for post-mortem trace analysis.

Versions:4.6.4
License:LGPLv2.1
Categories:Trace Analysis, Visualiztion, performance
paraview

Paraview data analysis and visualization application.

Versions:5.1.0
License:http://www.paraview.org/paraview-license/
Categories:Visualization, data analysis
parmetis

ParMETIS – Parallel Graph Partitioning and Fill-reducing Matrix Ordering

Versions:4.0.3-intel-16.0.3; 4.0.3-intel-17.0.1
License:http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download
Categories:matrices, matrix, ordering, partitioning
pbh5tools

A swiss-army knife for interrogating PacBio HDF5 files (cmp.h5, bas.h5)

Versions:1.0
License:Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
Categories:bioinformatics
pdl

PDL turns Perl into a free, array-oriented, numerical language similar to IDL and MatLab.

Versions:2.016
License:The Perl 5 License (Artistic 1 & GPL 1)
Categories:Perl, arrays, data, numerical, scientific
pear

PEAR – Paired-End reAd mergeR

Versions:0.9.6
License:GPLv2
Categories:bioinformatics
perl-modules

Perl addin modules for use with Perl version 5.16.3.

Versions:1.0
License:GPLv2
Categories:bioinformatics
perlmods

Various CPAN modules

Versions:5.16.3
License:Perl Artistic License
Categories:
petpvc

PETPVC toolbox for partial volume correction of PET images.

Versions:1.2.4
License:Apache 2.0 https://github.com/UCL/PETPVC/blob/master/LICENSE.txt
Categories:PET image, image analysis, neuroimaging, partial volume correction
petsc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

Versions:3.7.4-impi; 3.8.4-ind64; 3.8.4; 3.10.3; 3.7.4; 3.10.3-impi
License:http://www.mcs.anl.gov/petsc/documentation/license.html
Categories:data structures, partial differential equations, scientific routines
pftools

The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.

Versions:2.4
Categories:bioinformatics
PGDSpider

An automated data conversion tool for connecting population genetics and genomics programs

Versions:2.1.1.0
License:BSD 3-Clause License, see LICENSE.txt
Categories:Conversion, Genomics, bioinformatics, genetics
pgi

Compiler suite.

Versions:19.1; 16.4
License:http://www.pgroup.com/doc/LICENSE.txt
Categories:Compiler, Development, debugger, profiler
pgplot

The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.

Versions:5.2.2
License:PGPLOT, Graphics Subroutine Library
Categories:
phrap_cross_match

cross_match is a general purpose utility for comparing any two DNA sequence sets using a ‘banded’ version of swat.

Versions:1.0
License:UNKNOWN
Categories:bioinformatics
phyloassigner

PhyloAssigner is a Perl pipeline for phylogenetic classification of amplicon pyrosequences.

Versions:6.166
License:GPL3
Categories:bioinformatics
phylosift

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

Versions:1.0.1
License:GPL3
Categories:bioinformatics
phyml

PhyML is a software package which primary task that is to estimate maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.

Versions:3.2.20160530
License:GPL3
Categories:bioinformatives phylogeny
picard

A set of tools for working with high-throughput sequencing data

Versions:2.4.1; 1.76; 2.3.0; 2.18.17; 1.79
License:MIT License, Apache License V2.0
Categories:bioinformatics
piler-cr

PILERCR is public domain software for finding CRISPR repeats.

Versions:1.06
License:GPLv3
Categories:bioinformatics
pilon

Pilon is a software tool which can be used to: Automatically improve draft assemblies, Find variation among strains, including large event detection

Versions:1.22
License:Broad Institute Software License Agreement
Categories:bioinformatics
pio

A high-level Parallel I/O Library for structured grid applications

Versions:1.10.0 with impi/2017.1.132
Categories:Core, Development, library
platanus

PLATform for Assembling NUcleotide Sequences

Versions:1.2.4
License:???
Categories:Genomics
Platypus

A variant caller

Versions:0.8.1
Categories:Development, bioinformatics, library
plink

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Versions:2.00a2; 2.0; 1.9
License:GPLv3
Categories:bioinformatics
plumed-qe

Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.

Versions:6.2
License:http://www2.mmm.ucar.edu/wrf/users/public.html
Categories:ab initio quantum chemistry, electronic structure, materials modeling
PnetCDF

Parallel netCDF: A Parallel I/O Library for NetCDF File Access

Versions:1.10.0 with impi/2017.1.132; 1.9.0 with intel/17.0.1
Categories:Development Tools
popoolation2

PoPoolation2 allows comparision of allele frequencies for SNPs between two or more populations and identification of significant differences.

Versions:1.201
License:Unknown
Categories:bioinformatics
postgresql

PostgreSQL is an object-relational database management system (ORDBMS) based on POSTGRES, Version 4.21, developed at the University of California at Berkeley Computer Science Department. POSTGRES pioneered many concepts that only became available in some commercial database systems much later. PostgreSQL is an open-source descendant of this original Berkeley code.

Versions:11.0
License:https://opensource.org/licenses/postgresql
Categories:Relational Database, SQL
povray

High-quality raytracer for 3D graphics.

Versions:3.7
Categories:
pplacer

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

Versions:1.1.alpha18
License:GPL3
Categories:bioinformatics
prank

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

Versions:150803
License:GPLv3
Categories:bioinformatics
Current page: 9
Total pages: 13
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