A | B | C | |
Database | Features | Link | |
BAR | Database of plant genes and proteins | http://bar.utoronto.ca/ | |
Bgee | Gene expression patterns | https://bgee.org/ | |
Ensembl | Genome browser of vertebrates, includes tools for identification of homology | https://www.ensembl.org/index.html | |
Entrez | Gene sequences and structures | https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html | |
FlyBase | Genome and proteome of the model insect D. melanogaster | https://flybase.org/ | |
GeneCards | Human gene function, genomics, transcription factor binding sites and protein products | https://www.genecards.org/ | |
GenBank | Annotated DNA sequences | https://www.ncbi.nlm.nih.gov/genbank/ | |
NCBI | Collection of databases for molecular biology and medicine providing many bioinformatics tools and services | https://www.ncbi.nlm.nih.gov/ | |
PomBase | Genome and proteome of the model yeast S. pombe | https://www.pombase.org/ | |
TAIR | Genome and proteome of the model plant A. thaliana | https://www.arabidopsis.org/ | |
WormBase | Genome and proteome of the model nematode C. elegans | https://wormbase.org//#012-34-5 | |
Xenbase | Genome and proteome of the model amphibian X. laevis | http://www.xenbase.org/entry/ |
A | B | C | |
Database | Features | Link | |
CATH | Classification of protein domains based on their structure, functionality, and evolution | https://www.cathdb.info/ | |
FSSP | Classification of protein domains based on their structural similarity | https://archive.ph/20121222235655/http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-id+5Ti2u1RffMj+-lib+FSSP | |
Gene Ontology | Unified annotation of molecular function, biological processes, and cellular components of proteins | http://geneontology.org/ | |
Human Protein Atlas | Information on human protein and their link with diseases | https://www.proteinatlas.org/ | |
InterPro | Classification of proteins domains and functional sites | https://www.ebi.ac.uk/interpro/ | |
KEGG | Protein function and biological pathways | https://www.genome.jp/kegg/ | |
PDB | 3D structures of proteins | https://www.rcsb.org/ | |
Pfam | Information about protein families and domains | http://pfam.xfam.org/ | |
PHAROS | Centralizes literature for human proteins | https://pharos.nih.gov/ | |
PRINTS | Protein fingerprints classification database | http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ | |
PROSITE | Protein family database | https://prosite.expasy.org/ | |
SCOP | Classification of protein domains based on their structure, functionality and evolution | https://scop.mrc-lmb.cam.ac.uk/ | |
SUPERFAMILY | Protein structure and functions | https://supfam.org/ | |
UniProt | General information on proteins, including sequence, structure, classification, function, subcellular localization and simple homology identification | https://www.uniprot.org/uniprot/ |
A | B | C | |
BLAST | Protein or DNA homology search in NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi | |
BLAT | Sequence homology search in animal genomes | https://genome.ucsc.edu/cgi-bin/hgBlat | |
Ensembl | Genome browser of vertebrates, includes tools for identification of homology | https://m.ensembl.org/index.html | |
FASTA | Sequence search against protein databases and sequence alignment | https://www.ebi.ac.uk/Tools/sss/fasta/ | |
HMMER | Gene and protein homology search | http://hmmer.org/ | |
Pfam | Protein families and domains, includes tools for identification of homology | http://pfam.xfam.org/ | |
SSAHA | DNA sequence search and alignment | https://www.sanger.ac.uk/tool/ssaha/ | |
UniProt | General information on proteins, including tools for identification of similartity | https://www.uniprot.org/uniprot/ |
A | B | C | |
Software | Features | Link | |
BAli-Phy | Multiple sequence alignment of nucleotide and amino acid sequences, and phylogenetic analysis using BI | http://www.bali-phy.org | |
CLUSTAL Omega* | Speed-oriented multiple sequence alignment for nucleotide or amino acid data, suitable for large datasets | https://www.ebi.ac.uk/Tools/msa/clustalo/ | |
CLUSTALW* | Multiple sequence alignment for nucleotide or amino acid data | https://www.genome.jp/tools-bin/clustalw | |
CONTRAlign (ProbCons) | Accuracy-oriented multiple sequence alignment for amino acid data | http://contra.stanford.edu/contralign/ | |
Kalign* | Multiple sequence alignment for nucleotide or amino acid data, suitable for large datasets | https://www.ebi.ac.uk/Tools/msa/kalign/ | |
MAFFT* | Accuracy-oriented multiple sequence alignment for nucleotide or amino acid data | https://mafft.cbrc.jp/alignment/server/ | |
MUSCLE* | Multiple sequence alignment for nucleotide or amino acid data | https://www.ebi.ac.uk/Tools/msa/muscle/ | |
PASTA | Speed-oriented multiple sequence alignment for nucleotide or amino acid data, designed for very large datasets | https://bioinformaticshome.com/tools/msa/descriptions/PASTA.html | |
PRANK/ WebPRANK* | Speed-oriented multiple sequence alignment for nucleotide or amino acid data, should be preferred for close sequences and large datasets | http://wasabiapp.org/software/prank/ https://www.ebi.ac.uk/goldman-srv/webprank/ | |
SATé | Software package for multiple sequence alignments and phylogenetic inference | https://phylo.bio.ku.edu/software/sate/sate.html | |
T-COFFEE* | Accuracy-oriented multiple sequence alignment of nucleotide and amino acid sequences | http://tcoffee.crg.cat/ | |
UPP | Speed-oriented multiple sequence alignment of nucleotide and amino acid sequences, designed for very large data sets | https://github.com/smirarab/sepp. |
A | B | C | |
Software | Features | Link | |
AliStat | Quantification of alignment completeness for alignment refinement | https://github.com/thomaskf/AliStat | |
BMGE | Selection of informative regions on multiple sequence alignments | https://gitlab.pasteur.fr/GIPhy/BMGE | |
GBlocks | Selection of informative regions on multiple sequence alignments | http://molevol.cmima.csic.es/castresana/Gblocks.html | |
Guidance 2* | Selection of informative regions on multiple sequence alignments | http://guidance.tau.ac.il/ | |
Noisy | Selection of informative regions on multiple sequence alignments | http://www.bioinf.uni-leipzig.de/Software/noisy/ | |
trimAl | Selection of informative regions on multiple sequence alignments | http://trimal.cgenomics.org/ |
A | B | C | |
Software | Features | Link | |
APE | R-written package for molecular phylogenetics using distance-based methods | http://ape-package.ird.fr | |
BAli-Phy | Phylogenetic inference using BI | http://www.bali-phy.org | |
BayesTraits | Phylogenetic inference and other evolutionary analyses using BI | http://www.evolution.reading.ac.uk/BayesTraitsV4.0.0/BayesTraitsV4.0.0.html | |
FastMe* | Phylogenetic inference using distance methods | http ://www.atgc-montpellier.fr/fastme/ | |
GARLI | Phylogenetic inference using ML | http ://evomics.org/resources/software/molecular-evolution-software/garli/ | |
HYPHY* | Phylogenetic inference using ML and distance methods | https ://www.hyphy.org/ | |
IQ-TREE2* | Phylogenetic inference using ML, including model selection and a very fast bootstrapping method | http ://www.iqtree.org/ http://iqtree.cibiv.univie.ac.at/ | |
MEGA | Sequence alignment, model selection, phylogenetic analysis using distance methods, MP and ML, and other evolutionary analyses | https://www.megasoftware.net/ | |
MrBayes | Phylogenetic inference using BI and diverse evolutionary analyses including ancestral states reconstruction and time calibration | http://nbisweden.github.io/MrBayes/ | |
PAML | phylogenetic inference using ML, estimation of selection strength, ancestral states reconstruction and other evolutionary analyses | http://abacus.gene.ucl.ac.uk/software/paml.html | |
PAUP | Phylogenetic inference using MP and ML | http://paup.phylosolutions.com/ | |
PHYLIP | Phylogenetic inference using MP, distance methods and ML | https ://evolution.genetics.washington.edu/phylip.html | |
PhyloBayes | Phylogenetic inference with protein data using BI using a specific probabilistic model | http ://www.atgc-montpellier.fr/phylobayes/ | |
PhyML* | Phylogenetic inference using ML, ancestral states reconstruction and various evolutionary analyses | http://atgc.lirmm.fr/phyml/ | |
PyCogent | Phylogenetic inference, tree drawing, various evolutionary analyses including partition models and ancestral states reconstruction | https ://github.com/pycogent/pycogent | |
RAxML* | Phylogenetic inference using ML | https://cme.h-its.org/exelixis/web/software/raxml/ | |
SeaView | Sequence alignment and phylogenetic inference using MP, NJ and ML | http://doua.prabi.fr/software/seaview | |
SplitsTree | Phylogenetic inference for unrooted trees and phylogenetic networks | https ://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/splitstree/ |
A | B | C | |
Software | Features | Link | |
ModelFinder | Fast model selection with a model of rate heterogeneity between sites (nucleotide, amino acids, codons) | Implemented in IQ-TREE | |
ModelTest / jModelTest | Nucleotide substitution model selection | http://evomics.org/resources/software/molecular-evolution-software/modeltest/ | |
PartitionFinder 2 | Molecular evolution model selection (nucleotide or amino acids) | http://www.robertlanfear.com/partitionfinder/ | |
ProtTest | Aminoacid substitution model selection | https://github.com/ddarriba/prottest3 | |
SMS | Molecular evolution model selection included in PhyML (nucleotide, amino acids) | http://www.atgc-montpellier.fr/sms/ |
A | B | C | |
Software | Features | Link | |
ETE Toolkit | Visualization and analysis of phylogenetic trees | http://etetoolkit.org/ | |
FigTree | Graphic software for phylogenetic trees | http://tree.bio.ed.ac.uk/software/figtree/ | |
ITOL* | Visualization and annotation of phylogenetic trees | https://itol.embl.de/ | |
MEGA | Sequence alignment, model selection, phylogenetic analysis, includes tree visualization and annotation tools | https://www.megasoftware.net/ | |
SeaView | Sequence alignment and phylogenetic inference, includes tree visualization and annotation tools | http://doua.prabi.fr/software/seaview |
A | B | C | |
Software | Features | Link | |
BayesTraits | Evolutionary analyses using Bayesian inference | http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.5/BayesTraitsV3.0.5.html | |
BEAST | Diverse evolutionary analyses using Bayesian inference, including phylogenetic analysis, calibration and molecular clock | http://www.beast.community | |
Mega | Sequence alignment, model selection, phylogenetic analysis (parsimony, distance methods) | https://www.megasoftware.net/ | |
Mesquite | Comparative analyses and statistics | http://www.mesquiteproject.org/ | |
MrBayes | Bayesian phylogenetic inference, ancestral states reconstruction, phylogenetic calibration… | http://nbisweden.github.io/MrBayes/ | |
Ohnologs | Database of vertebrate ohnologues, resulting from whole genome duplications | http://ohnologs.curie.fr/ | |
Timetree | Time calibration of phylogenetic trees | http://www.timetree.org/ |
A | B | C | |
Software | Features | Link | |
BayesTraits | Evolutionary analyses using Bayesian inference | http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.5.html | |
BEAST | Diverse evolutionary analyses using BI, including phylogenetic analysis, ancestral states reconstruction, time-calibration and molecular clock | http://www.beast.community | |
Mega | Sequence alignment, phylogenetic analysis and diverse analyses including ancestral states reconstruction | https://www.megasoftware.net/ | |
Mesquite | Comparative analyses and statistics | http://www.mesquiteproject.org/ | |
MrBayes | Bayesian phylogenetic inference, ancestral states reconstruction, phylogenetic calibration… | http://nbisweden.github.io/MrBayes/ | |
PAML | Maximum likelihood phylogenetic inference, estimation of selection strength, ancestral states reconstruction and other analyses | http://abacus.gene.ucl.ac.uk/software/paml.html | |
RASP | Ancestral states reconstruction | http://mnh.scu.edu.cn/soft/blog/RASP/index.html |
A | B | C | |
Software | Features | Link | |
Copycat | Co-evolution studies | http://www.cophylogenetics.com/ | |
Core-PA | Co-evolution studies | http://pacosy.informatik.uni-leipzig.de/49-1-CoRe-PA.html | |
Jane | Co-evolution studies | https://www.cs.hmc.edu/~hadas/jane/ | |
TreeMap | Co-evolution studies | https://sites.google.com/site/cophylogeny/treemap |
A | B | C | |
Software | Features | Link | |
BAR | Database of plant genes and proteins | http://bar.utoronto.ca/ | |
CAFE | Gene family evolution | https://github.com/hahnlab/CAFE5 | |
CoGE | Comparative genomics analyses | https://genomevolution.org/coge/ | |
Ensembl | Genome browser of vertebrates, includes tools for identification of homology | https://www.ensembl.org/index.html | |
Entrez | Gene sequences and structures | https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html | |
FlyBase | Genome and proteins of the model insect D. melanogaster | https://flybase.org/ | |
GenBank | Annotated DNA sequences | https://www.ncbi.nlm.nih.gov/genbank/ | |
HGT-Finder | Horizontal gene transfer finding | http://cys.bios.niu.edu/HGTFinder/ HGTFinder.tar.gz | |
Ohnologs | Database of vertebrate ohnologues, resulting from whole genome duplications | http://ohnologs.curie.fr/ | |
PomBase | Genes and proteins of the model yeast S. pombe | https://www.pombase.org/ | |
TAIR | Genome and proteins of the model plant A. thaliana | https://www.arabidopsis.org/ | |
WormBase | Genome and proteins of the model nematode C. elegans | https://wormbase.org//#012-34-5 | |
Xenbase | Genome and proteins of the model amphibian X. laevis | http://www.xenbase.org/entry/ |
A | B | C | |
Software | Features | Link | |
DNAsp | Analysis of DNA polymorphism | http://www.ub.edu/dnasp/ | |
Genepop | Population genetics analyses | https://genepop.curtin.edu.au/ | |
SNiplay | SNP detection and other population genetics analyses | https://sniplay.southgreen.fr/cgi-bin/home.cgi | |
Arlequin | Population genetics analyses | http://cmpg.unibe.ch/software/arlequin35/ |
A | B | C | |
Software | Features | Link | |
Alpha fold | Protein structure prediction from amino-acid sequence | https://alphafold.ebi.ac.uk/ | |
FoRSA | Protein structure prediction | http://www.bo-protscience.fr/forsa/ | |
HHPred | Protein structure prediction | https://toolkit.tuebingen.mpg.de/tools/hhpred | |
I-TASSER | Protein structure prediction | https://zhanglab.dcmb.med.umich.edu/I-TASSER/ | |
PDB | 3-dimensional structures of proteins | https://www.rcsb.org/ | |
Prints | Protein fingerprints classification | http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ | |
PyMol | 3D visualization of molecules and diverse analyses on protein structures | https://pymol.org/2/ |