Institut Pasteur blank vertical divider clipart blank DBC blank vertical divider clipart blank CRBIP blank vertical divider clipart blank GIPhy

G I Phy GIPhy

Genome Informatics and Phylogenetics
 


Presentation

Welcome to the homepage of GIPhy, the genomic taxonomy expertise group of the Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP). GIPhy is highly involved in bioinformatics developments and 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

AA models 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 PhyloM
  phylogenetic markers suited for the phylogenetic analysis of specific phyla
http://giphy.pasteur.fr/PhyloM

Programs and Tools

AlienDiscover AlienDiscover
  inferring alien oligonucleotides (adapters, primers, ...) from short sequencing reads
https://gitlab.pasteur.fr/GIPhy/AlienDiscover
AlienRemover AlienRemover
  removing contaminating reads from High-Throughput Sequencing data
https://gitlab.pasteur.fr/GIPhy/AlienRemover
AlienTrimmer AlienTrimmer
  clipping and trimming High-Throughput Sequencing reads
https://research.pasteur.fr/en/software/alientrimmerbioconda
BMGE BMGE
  selecting characters from a multiple sequence alignment for phylogenetic inference
https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropybioconda
C2A/A2C C2A/A2C
  two tools for translating and back-translating codon and amino-acid sequence files, respectively
https://gitlab.pasteur.fr/GIPhy/C2A.A2C
Concatenate Concatenate
  building a supermatrix of characters by concatenating multiple sequence alignments
https://gitlab.pasteur.fr/GIPhy/Concatenate
contig_info contig_info
  estimating standard descriptive statistics from contig sequences
https://gitlab.pasteur.fr/GIPhy/contig_info
DNA2ORF DNA2ORF
  efficient genome partitioning into open reading frames
https://gitlab.pasteur.fr/GIPhy/DNA2ORF
eCDS eCDS
  extracting coding sequences from a FASTA-formatted contig sequence file
https://gitlab.pasteur.fr/GIPhy/eCDS
eFASTA eFASTA
  extracting nucleotide segments from a FASTA-formatted file
https://gitlab.pasteur.fr/GIPhy/eFASTAbioconda
FASTA2AGP FASTA2AGP
  creating AGP files from FASTA-formatted scaffold sequence files
https://gitlab.pasteur.fr/GIPhy/FASTA2AGP
fastq_info fastq_info
  estimating standard descriptive statistics from FASTQ files
https://gitlab.pasteur.fr/GIPhy/fastq_info
findSynapomorphies findSynapomorphies
  finding characters shared by a group of aligned sequences
https://gitlab.pasteur.fr/GIPhy/findSynapomorphies
fqCleanER fqCleanER
  FASTQ file Cleaning and Enhancing Routine
https://research.pasteur.fr/en/tool/fqcleaner
fq2dna fq2dna
  genome de novo assembly from raw paired-end FASTQ files
https://research.pasteur.fr/en/tool/fq2dna
gbk2ENA gbk2ENA
  converting Genbank files into EMBL-like files suitable for submission to the ENA
https://gitlab.pasteur.fr/GIPhy/gbk2ENA
GenoLayout GenoLayout
  creating figures showing linear maps between genomes
https://gitlab.pasteur.fr/GIPhy/GenoLayout
GenoMed GenoMed
  determining the medoid of a set of genomes
https://gitlab.pasteur.fr/GIPhy/GenoMed
Gklust Gklust
  fast genome sequence clustering
https://gitlab.pasteur.fr/GIPhy/Gklust
HCAP HCAP
  cropping reads to reach homogeneous composition among position
https://gitlab.pasteur.fr/GIPhy/HCAP
JolyTree JolyTree
  inferring distance-based phylogenetic trees from unaligned genome sequences
https://research.pasteur.fr/fr/software/jolytreebiocondabioconda
MSAshrink MSAshrink
  Multiple Sequence Alignment shrinking
https://gitlab.pasteur.fr/GIPhy/MSAshrink
MSTclust MSTclust
  Minimum Spanning Tree-based clustering
https://gitlab.pasteur.fr/GIPhy/MSTclust
OGRI OGRI
  estimating Overall Genome Relatedness Indices
https://gitlab.pasteur.fr/GIPhy/OGRI
RepeatPlot RepeatPlot
  creating figures that represent the positions of long repeats in a chromosome
https://gitlab.pasteur.fr/GIPhy/RepeatPlot
REQ REQ
  estimating branch supports in distance-based phylogenetic trees
https://research.pasteur.fr/fr/b/_LVbiocondabiocondabioconda
ROCK ROCK
  fast and accurate digital normalization of high-thoughput sequencing reads
https://research.pasteur.fr/en/software/rock
SAM2MSA SAM2MSA
  building a multiple sequence alignment well-suited for phylogenetic analysis from read mapping data
https://gitlab.pasteur.fr/GIPhy/SAM2MSA
SimiPlot SimiPlot
  creating figures showing overall similarity between genomes
https://gitlab.pasteur.fr/GIPhy/SimiPlot
wgetENAHTS wgetENAHTS
  downloading FASTQ files from the ENA repositories
https://gitlab.pasteur.fr/GIPhy/wgetENAHTS
wgetGenBankWGS wgetGenBankWGS
  downloading genome assembly FASTA files from the GenBank or RefSeq repositories
https://gitlab.pasteur.fr/GIPhy/wgetGenBankWGS
YACO 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 GIPhy