pipelines and tools for the processing of ancient and modern HTS data

Phylogenetic Analysis by Maximum Likelihood (PAML)

PAN Blend config package

PAN Blends tasks for tasksel

Parametric clustering of genomic and transcriptomic features

parallel command processing using OpenMP

parallel fastq-dump wrapper

Parallel Visualization Application

Parsimonious Insertion of unclassified sequences into phylogenetic trees

Test data for parsinsert

rapid core genome multi-alignment

rapid alignment of short sequences to large databases

processing Pacific Biosciences binary alignment/map files

sequence consensus using directed acyclic graphs

simulator for PacBio sequencing reads

Preparation of protein structures for electrostatics calculations

tools for manipulating and editing PDB files

Graphical design of primers for PCR

efficient mapping of short reads with periodic spaced seeds

GUI for uncertainty treatment and variabilities management

build and search protein and DNA generalized profiles

phylogenetic analysis with space/time models

PHI test and other tests of recombination

binning/clustering newick trees by topology

package of programs for inferring phylogenies

Fast and Accurate Estimation of Evolutionary Distances

Phylogenetic estimation using Maximum Likelihood

sample sequence alignment corresponding to phylogeny

simple analyses or modifications on both phylogenetic trees and data matrices

UNIX-style phylogenetic analyses on trees and sequences

Command line tools to manipulate SAM and BAM files

lossless compression of Nanopore files

SAT solver with proof and core support

pipeline for checkpointed and distributed RNA-seq analyses

genomic repeat analysis

software for finding CRISPR repeats

automated genome assembly improvement and variant detection tool

Collection of tools to annotate genomes using long read transcriptomics data

Examples and test data for pinfish

software pipeline for performing genome wide association studies

Profile based Illumina pair-end Reads Simulator

profile basd Illumina pair-end Reads Simulator (example data)

profile basd Illumina pair-end Reads Simulator (profile data)

Identifies gene fusions in RNA sequencing data

Script for the automatic testing of R packages

GDAL add-on tools to perform useful raster processing

Plasmid Constellation Network project

create a sharp image of a planetary system object (moon, sun, planets)

Gravitation simulation of planetary bodies

mapping-based, assembly-assisted plasmid identification tool