-
PHYLIP
- Referenced in 97 articles
[sw07694]
- free package of programs for inferring phylogenies. It is distributed as source code, documentation files...
-
BEAST
- Referenced in 44 articles
[sw12588]
- molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models ... used as a method of reconstructing phylogenies but is also a framework for testing evolutionary...
-
ape
- Referenced in 55 articles
[sw04569]
- using mean path lengths and penalized likelihood. Phylogeny estimation can be done with...
-
MrBayes
- Referenced in 49 articles
[sw07715]
- MrBayes: Bayesian Inference of Phylogeny. MrBayes is a program for Bayesian inference and model choice...
-
RAxML
- Referenced in 34 articles
[sw07716]
- Parallel inference of a 10.000-taxon phylogeny with maximum likelihood. Inference of large phylogenetic trees ... that RAxML outperforms the currently fastest statistical phylogeny programs (MrBayes, PHYML) in terms of speed...
-
Seq-Gen
- Referenced in 30 articles
[sw08310]
- nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process...
-
SplitsTree
- Referenced in 30 articles
[sw12234]
- indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing...
-
phytools
- Referenced in 13 articles
[sw10003]
- taxa; reducing a phylogeny to its backbone tree; dropping tips or adding tips to special ... character state per edge; estimating a phylogeny using the least squares method; simulating birth-death...
-
Bali-phy
- Referenced in 9 articles
[sw16614]
- simultaneous bayesian inference of alignment and phylogeny. Summary: BAli-Phy is a Bayesian posterior sampler ... explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates ... information in shared insertion/deletions to help infer phylogenies. Availability: Software is available for download...
-
PhyloNet
- Referenced in 9 articles
[sw20725]
- analyzing and reconstructing reticulate evolutionary relationships. BACKGROUND: Phylogenies, i.e., the evolutionary histories of groups ... software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which...
-
CVTree3
- Referenced in 7 articles
[sw22015]
- Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. A faithful phylogeny...
-
INDELible
- Referenced in 7 articles
[sw23043]
- sequence evolution. Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies...
-
PhyML
- Referenced in 9 articles
[sw10915]
- software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences...
-
ASTRAL-II
- Referenced in 9 articles
[sw20492]
- genes. Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have...
-
MultiLoc2
- Referenced in 8 articles
[sw22456]
- MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BACKGROUND: Knowledge...
-
DPRml
- Referenced in 4 articles
[sw12590]
- DPRml: distributed phylogeny reconstruction by maximum likelihood. Motivation: In recent years there has been increased ... platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses...
-
Statalign
- Referenced in 4 articles
[sw16609]
- phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions ... samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying...
-
Phylomatic
- Referenced in 4 articles
[sw22217]
- relationships among taxa. Any set of stored phylogenies, or a user-supplied ... chosen as the basis for the returned phylogeny, and several output formats for the tree...
-
SEAVIEW
- Referenced in 4 articles
[sw22985]
- graphic tools for sequence alignment and molecular phylogeny. SEAVIEW and PHYLO_WIN are two graphic ... anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail...
-
PHYLO_WIN
- Referenced in 4 articles
[sw22986]
- graphic tools for sequence alignment and molecular phylogeny. SEAVIEW and PHYLO_WIN are two graphic ... anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail...