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

G I Phy 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 Research and Resource Centre for Scientific Informatics, Institut Pasteur, Paris, France. 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

AlienRemover   ‖   removing contaminating reads from High-Throughput Sequencing data
https://gitlab.pasteur.fr/GIPhy/AlienRemover

AlienTrimmer   ‖   clipping and trimming High-Throughput Sequencing reads
https://research.pasteur.fr/en/software/alientrimmerbioconda

BMGE   ‖   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-entropybioconda

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

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

contig_info   ‖   estimating standard descriptive statistics from contig sequences
https://gitlab.pasteur.fr/GIPhy/contig_info

DNA2ORF   ‖   efficient genome partitioning into open reading frames
https://gitlab.pasteur.fr/GIPhy/DNA2ORF

eCDS   ‖   extracting coding sequences from a FASTA-formatted contig sequence file
https://gitlab.pasteur.fr/GIPhy/eCDS

eFASTA   ‖   extracting nucleotide segments from a FASTA-formatted file
https://gitlab.pasteur.fr/GIPhy/eFASTAbioconda

FASTA2AGP   ‖   creating AGP files from FASTA-formatted scaffold sequence files
https://gitlab.pasteur.fr/GIPhy/FASTA2AGP

fastq_info   ‖   estimating standard descriptive statistics from FASTQ files
https://gitlab.pasteur.fr/GIPhy/fastq_info

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

fqCleanER   ‖   FASTQ file Cleaning and Enhancing Routine
https://research.pasteur.fr/en/tool/fqcleaner

fq2dna   ‖   genome de novo assembly from raw paired-end FASTQ files
https://research.pasteur.fr/en/tool/fq2dna

Gklust   ‖   fast genome sequence clustering
https://gitlab.pasteur.fr/GIPhy/Gklust

GenoLayout   ‖   creating figures showing linear maps between genomes
https://gitlab.pasteur.fr/GIPhy/GenoLayout

GenoMed   ‖   determining the medoid of a set of genomes
https://gitlab.pasteur.fr/GIPhy/GenoMed

JolyTree   ‖   inferring distance-based phylogenetic trees from unaligned genome sequences
https://research.pasteur.fr/fr/software/jolytreebiocondabioconda

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

MSAshrink   ‖   Multiple Sequence Alignment shrinking
https://gitlab.pasteur.fr/GIPhy/MSAshrink

MSTclust   ‖   Minimum Spanning Tree-based clustering
https://gitlab.pasteur.fr/GIPhy/MSTclust

OGRI   ‖   estimating Overall Genome Relatedness Indices
https://gitlab.pasteur.fr/GIPhy/OGRI

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

RepeatPlot   ‖   creating figures that represent the positions of long repeats in a chromosome
https://gitlab.pasteur.fr/GIPhy/RepeatPlot

ROCK   ‖   fast and accurate digital normalization of high-thoughput sequencing reads
https://research.pasteur.fr/en/software/rock

SAM2MSA   ‖   building a multiple sequence alignment well-suited for phylogenetic analysis from read mapping data
https://gitlab.pasteur.fr/GIPhy/SAM2MSA

SimiPlot   ‖   creating figures showing overall similarity between genomes
https://gitlab.pasteur.fr/GIPhy/SimiPlot

wgetENAHTS   ‖   downloading FASTQ files from the ENA repositories
https://gitlab.pasteur.fr/GIPhy/wgetENAHTS

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

YACO   ‖   yet another contig ordering
https://gitlab.pasteur.fr/GIPhy/YACO

Supplementary Data

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


GIPhy