BIOS 477/877 Bioinformatics and Molecular Evolution (3 credits)
HOME
Schedule
Links
MYUNL
Moriyama Lab
[Last updated: January 20, 2024]
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)
Phylogeny
IQ-TREE
PhyML
RAxML: Randomized Axelerated Maximum Likelihood (and other software from Exelixis Lab)
FastTree 2: Approximately-maximum likelihood trees for large alignments
CIPRES: Cyberinfrastructure for Phylogenetic Research (including RAxML, MrBayes, GARLI)
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
SplitsTreeCE (early release, community edition of SplitsTree, replacing SplitsTree4 and Dendroscope3)
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
NJplot
Phylo.io: A web app and library for visualising and comparing phylogenetic trees
Phylo.io (a newer version)
PhyloWidget: web-based visualizations for the tree of life
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