Institut Pasteur blankvertical divider clipartblank C3BI blankvertical divider clipartblank Bioinformatics and Biostatistics Hub blankvertical divider clipartblank GIPhy

GIPhy GIPhy

Groupe d'Inférence Phylogénétique

Genome Informatics and Phylogenetics


Presentation

Welcome to the homepage of GIPhy, one of the expert groups of the Bioinformatics and Biostatistics Hub from the C3BI, Institut Pasteur, Paris, France. The group GIPhy is highly involved in scientific research topics focusing on biological classifications. Therefore, projects regarding important themes such as systematics, taxonomy, homology and related fields are specifically addressed by the members of this dedicated group.

Institutional webpage

More details about GIPhy (members, main projects, publication list): https://tinyurl.com/0-GIPhy-0

Databases and Datasets

Empirical Models of Amino Acid Substitution || a complete list of amino acid replacement matrices for model-based sequence evolution analyses
http://giphy.pasteur.fr/empirical-models-of-amino-acid-substitution

PhyloM || phylogenetic markers (along with multiple sequence alignments and position specific scoring matrices) that are well-suited for the phylogenetic analysis of specific phyla
http://giphy.pasteur.fr/PhyloM

RVDB-prot || reference viral coding sequence and associated HMM database developed for enhancing virus detection from High-Throughput Sequencing data
https://rvdb-prot.pasteur.fr

Programs and Tools

AlienTrimmer || a tool for clipping and trimming High-Throughput Sequencing reads
https://research.pasteur.fr/en/software/alientrimmer

BMGE || a tool for selecting characters or encoding character states from a multiple sequence alignment for phylogenetic inference
https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy

C2A/A2C || two tools for translating and back-translating codon and amino-acid sequence files, respectively
https://gitlab.pasteur.fr/GIPhy/C2A.A2C

Concatenate || a tool for building a supermatrix of characters by concatenating multiple sequence alignments
https://gitlab.pasteur.fr/GIPhy/Concatenate

contig_info || a tool for estimating standard descriptive statistics from contig sequences
https://gitlab.pasteur.fr/GIPhy/contig_info

eFASTA || a tool for extracting a nucleotide segment from a FASTA-formatted file
https://gitlab.pasteur.fr/GIPhy/eFASTA

FASTA2AGP || a tool for creating an AGP file from a FASTA-formatted scaffold sequence file
https://gitlab.pasteur.fr/GIPhy/FASTA2AGP

findSynapomorphies || a tool for finding characters shared by a group of aligned sequences
https://gitlab.pasteur.fr/GIPhy/findSynapomorphies

Gklust || a tool for fast genome sequence clustering
https://gitlab.pasteur.fr/GIPhy/Gklust

JolyTree || a tool for inferring distance-based phylogenetic trees from unaligned genome sequences   bioconda bioconda
https://research.pasteur.fr/fr/software/jolytree

gbk2ENA || a tool for converting Genbank files into EMBL-like files suitable for submission to the ENA
https://gitlab.pasteur.fr/GIPhy/gbk2ENA

REQ || a tool for estimating branch supports in distance-based phylogenetic trees   bioconda bioconda
https://research.pasteur.fr/fr/tool/rεq-assessing-branch-supports-oƒ-a-distance-based-phylogenetic-tree-with-the-rate-oƒ-elementary-quartets

wgetGenBankWGS || a tool for downloading genome assembly FASTA files from the GenBank or RefSeq repositories
https://gitlab.pasteur.fr/GIPhy/wgetGenBankWGS

Supplementary Data

Supplementary data accompanying some of our published analyses
https://giphy.pasteur.fr/data