BIOS 477/877 Bioinformatics and Molecular Evolution (3 credits)

[Last updated: January 13, 2025]

• Multiple Sequence Alignment
• ClustalW/ClustalX/Clustal Omega
• MUSCLE by Robert Edgar
• MAFFT by Kazutaka Katoh
• T-Coffee (including M-Coffee, Expresso, etc.)
• Kalign2
• PRALINE
• PROMALS
• PROMALS3D
• ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
• ProbCons @ Phylogeny.fr
• CONTRAlign: CONditional TRAining for Protein Sequence Alignment
• Probalign: Multiple sequence alignment using partition function posterior probabilities
• MSAProbs: Parallel and accurate multiple sequence alignment
• QuickProbs 2: faster successor of MSAProbs
• PnpProbs: Progressive and non-progressive combined alignment method
• FSA: Fast Statistical Alignment (sourceforge version)
• COBALT: Constraint-based Multiple Alignment Tool at NCBI
• hmmalign (part of HMMER package, requires a profile HMM to be aligned against)
• Dialign by Burkhard Morgenstern
• DCA: Divide-and-Conquer Multiple Sequence Alignment by J. Stoye
• OPAL
• MultAlin by Florence Corpet
• PRANK: Phylogeny-aware progressive sequence alignment method
• PAGAN: Multiple sequence alignment using partial-order graphs (based on the principle same as PRANK)
• ProGraphMSA (similar to PAGAN, incorporates a graph-based sequence representation combined with the phylogeny-aware gap placement algorithm of PRANK)
• learnMSA: Learning and Aligning large Protein Families


• Simultaneous Alignment and Phylogeny
• SATé - Simultaneous Alignment and Tree Estimation
• PASTA - Practical Alignment using Saté and TrAnsitivity
• MAGUS: Multiple sequence Alignment using Graph clUStering
• UPP2 - Ultra-large alignments using Phylogeny-aware Profiles
• BAli-Phy: Baysian ALignment and Phylogeny estimation
• Canopy: Parallelised iterative search of optimal phylogeny and phylogeny-aware sequence alignment


• Alignment Visualization and Editors
• SuiteMSA: Visual Tool for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation
• ClustalX (GUI version of ClustalW with more functions)
• AliView (fast alignment editor/viewer)
• SeaView (including phylogenetic reconstruction/viewer)
• Jalview: a multiple alignment editor written in Java
• Wasabi: a powerful multiple sequence alignment browser (includes ancestral sequence reconstruction)
• MEGA: Molecular Evolutionary Genetics Analysis (includes an alignment editor)
• STRAP: Interactive Structure based Sequences Alignment Program
• Kalignvu: an lighweight viewer for multiple sequence alignments and phylogenetic trees
• Squint
• Se-Al (only for Mac OS X up to 10.6)
• BioEdit: Biological sequence alignment editor for Win95/98/NT/2K/XP/7
• GeneDoc: a multiple alignment editor for Windows


• Translated DNA Alignment
• TranslatorX
• RevTrans 2.0
• PAL2NAL
• tranalign (from EMBOSS server)
• tranalign (from another EMBOSS)


• Alignment Trimmming/Filtering
• Gblocks
• trimAl
• ClipKIT
• HmmCleaner
• PREQUAL
• Divvier


• Alignment Evaluation
• BAliBASE 4: Benchmark Alignment dataBASE (including bali_score)
• HOMSTRAD: Homologous Structure Alignment Database
• BENCH from MUSCLE (including BAliBASE, PREFAB, OXBENCH, and SABRE)
• Guidance2
• Veralign
• Mumsa
• AlignStat
• QuanTest


• Phylogeny Reconstruction
  • IQ-TREE
  • PhyML
  • RAxML: Randomized Axelerated Maximum Likelihood (and other software from Exelixis Lab)
  • RAxML-NG: Randomized Axelerated Maximum Likelihood (and other software from Exelixis Lab)
  • FastTree 2: Approximately-maximum likelihood trees for large alignments
  • MrBayes: Bayesian Inference of Phylogeny
  • Phylip
  • GARLI: Genetic Algorithm for Rapid Likelihood Inference
  • FastME: Fast and accurate phylogeny reconstruction algorithm based on the minimum-evolution principle
  • BioNJ: an improved version of the NJ algorithm based on a simple model of sequence data
  • SplitsTree: Software for computing phylogenetic networks
  • T-Rex: Tree and Reticulogram reconstruction
  
  
• Phylogeny Visualization
• FigTree: a graphical viewer of phylogenetic trees
• ITOL: Interactive Tree of Life
• IcyTree
• Evolview3
• TreeDyn: Towards dynamic graphics and annotations for analyses of trees
• Newick Display @ NGPhylogeny.fr
• NJplot
• Phylo.io: A web app and library for visualising and comparing phylogenetic trees
• Phylo.io (a newer version)
• ARB: a software environment for sequence data (including alignment/phylogeny viewers and more)
• Treevolution
• Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Tress (the successor to ATV)
• A list of phylogenetic tree visualization software


• Alignment to Phylogenetic Analysis Pipeline
  • CIPRES: Cyberinfrastructure for Phylogenetic Research (including mafft, BAli-Phy, RAxML, MrBayes, GARLI, PAUP, etc.)
  • NGPhylogeny.fr (including mafft, MUSCLE, Clustal Omega, BMGE, Gblocks, trimAL, PhyML, MrBayes, FastME, TNT, etc.)
  • Phylogeny.fr (including MUSCLE, ProbCons, T-Coffee, ClustalW, Gblocks, PhyML, NJ, BioNJ, MrBayes, TNT)
  • Phylomon2 (including MUSCLE, ClustalW, Lagan, MLagan, trimAl, PhyML, MrBayes, etc.)