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.
More details about GIPhy (members, main projects, publication list): https://tinyurl.com/0-GIPhy-0
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
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/alientrimmer
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-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 ‖ 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/eFASTA
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/jolytree
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-quartets
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 accompanying some of our published analyses
https://giphy.pasteur.fr/data