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G I Phy

Genome Informatics and Phylogenetics
 

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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

	Empirical Models of Amino Acid Substitution   a complete list of amino acid replacement matrices for model-based sequence evolution analyses https://giphy.pasteur.fr/empirical-models-of-amino-acid-substitution
	PhyloM   phylogenetic markers suited for the phylogenetic analysis of specific phyla https://giphy.pasteur.fr/PhyloM

Programs and Tools  

	AlienDiscover   inferring alien oligonucleotides (adapters, primers, ...) from short sequencing reads https://gitlab.pasteur.fr/GIPhy/AlienDiscover
	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
	ASSU   assembling SSU from whole genome high-throughput sequencing reads https://gitlab.pasteur.fr/GIPhy/ASSU
	BMGE   selecting characters 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
	COGniz   COG annotation of CDS https://gitlab.pasteur.fr/GIPhy/COGniz
	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
	delice   assessing delineation cutoff estimates https://gitlab.pasteur.fr/GIPhy/delice
	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
	gbk2ENA   converting Genbank files into EMBL-like files suitable for submission to the ENA https://gitlab.pasteur.fr/GIPhy/gbk2ENA
	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
	Gklust   fast genome sequence clustering https://gitlab.pasteur.fr/GIPhy/Gklust
	HCAP   cropping reads to reach homogeneous composition among position https://gitlab.pasteur.fr/GIPhy/HCAP
	JolyTree   inferring distance-based phylogenetic trees from unaligned genome sequences https://research.pasteur.fr/fr/software/jolytree
	LINtree   building prefix tree from LIN codes https://gitlab.pasteur.fr/GIPhy/LINtree
	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
	phyloMseek   searching and extracting PhyloM: bacteria universal single-copy genes https://gitlab.pasteur.fr/GIPhy/phyloMseek
	RepeatPlot   creating figures that represent the positions of long repeats in a chromosome https://gitlab.pasteur.fr/GIPhy/RepeatPlot
	REQ   estimating branch supports in distance-based phylogenetic trees https://research.pasteur.fr/fr/b/_LV
	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
	SWANI   Smith-Waterman-based Average Nucleotide Identity https://gitlab.pasteur.fr/GIPhy/SWANI
	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