- do****entation for
recent bioinformatic software including IQ-Tree, Phy
ML, and
RAxML. The real
substitution rates in a
protein depends not only on the identity...
- PMID 38374231.
Kozlov AM,
Darriba D,
Flouri T,
Morel B,
Stamatakis A (May 2019). "
RAxML-NG: A fast, scalable, and user-friendly tool for
maximum likelihood phylogenetic...
- Sets".
Molecular Biology and Evolution. 35 (2): 486–503. doi:10.1093/molbev/msx302. PMC 5850867. (compares
RAxML/Exa
ML, Phy
ML, IQ-TREE, and FastTree)...
- all of them from the
PHYLIP package, and for the
maximum likelihood: Phy
ML,
RAxML, DNAML, DNAMLK,
PROML and PROMLK, the four
latter methods are from the...
-
treedist program in the
PHYLIP suite offers this function, as does the
RAxML_standard package, the
DendroPy Python library (under the name "symmetric...
- ignored. Many
programs for
phylogenetic analyses,
including the commonly-used
RAxML and IQ-TREE programs, use the
phylip format or a
minor modification of that...
- can be com****tionally
expensive and
there are
newer methods such as the
RAxML rapid bootstrap (RBS), the Shimodaira–Hasegawa-like
approximate likelihood...
- 2307/2412116. ISSN 0039-7989. JSTOR 2412116.
Stamatakis A (November 2006). "
RAxML-VI-HPC:
maximum likelihood-based
phylogenetic analyses with
thousands of...
- ProbCons,
FastAligner (region-align+auto-reference) arb-parsimony & -NJ,
RAxML, PHYML, Phylip, FastTree2,
MrBayes Edits huge
alignments and trees. Supports...
- for
phylogeny reconstruction will
depend on
whether a
Maximum Likelihood (
ML),
Maximum Parsimony (MP), or
Bayesian Inference (BI)
method is appropriate...
