Software Item | Details | ||||||
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orthofinder | Accurate inference of orthologous gene groups made easy.
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p4 | P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.
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p4vasp | This software is Open Source. p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP).
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p7zip | p7zip is a port of 7za.exe, compression app, for POSIX systems like Unix.
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paml | PAML (for Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood.
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pandoc | Pandoc is open-source software, maintained by volunteers working in their free time. Please keep that in mind when asking for help.
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parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
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parallel-fastq-dump | parallel fastq-dump wrapper
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paraver | Expressive powerful and flexible trace visualizer for post-mortem trace analysis.
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paraview | Paraview data analysis and visualization application.
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parmetis | ParMETIS – Parallel Graph Partitioning and Fill-reducing Matrix Ordering
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pbh5tools | A swiss-army knife for interrogating PacBio HDF5 files (cmp.h5, bas.h5)
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pdl | PDL turns Perl into a free, array-oriented, numerical language similar to IDL and MatLab.
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pear | PEAR – Paired-End reAd mergeR
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perl-modules | Perl addin modules for use with Perl version 5.16.3.
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perlmods | Various CPAN modules
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petpvc | PETPVC toolbox for partial volume correction of PET images.
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petsc | PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
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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.
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PGDSpider | An automated data conversion tool for connecting population genetics and genomics programs
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pgi | Compiler suite.
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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.
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phrap_cross_match | cross_match is a general purpose utility for comparing any two DNA sequence sets using a ‘banded’ version of swat.
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phyloassigner | PhyloAssigner is a Perl pipeline for phylogenetic classification of amplicon pyrosequences.
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phylosift | PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.
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phyml | PhyML is a software package which primary task that is to estimate maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.
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picard | A set of tools for working with high-throughput sequencing data
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piler-cr | PILERCR is public domain software for finding CRISPR repeats.
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pilon | Pilon is a software tool which can be used to: Automatically improve draft assemblies, Find variation among strains, including large event detection
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pio | A high-level Parallel I/O Library for structured grid applications
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platanus | PLATform for Assembling NUcleotide Sequences
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Platypus | A variant caller
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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.
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plumed-qe | Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.
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PnetCDF | Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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popoolation2 | PoPoolation2 allows comparision of allele frequencies for SNPs between two or more populations and identification of significant differences.
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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.
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povray | High-quality raytracer for 3D graphics.
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pplacer | Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
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prank | PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
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Total pages: 13
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