:: DESCRIPTION
PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics, 26 (7), 962-3 2010 Apr 1
Phybase: An R Package for Species Tree Analysis
Liang Liu 1, Lili Yu
:: DESCRIPTION
Ultranet is designed to be an helpful tool for the analysis genomic data, or in general of any type of data that can be represented as a vector of features.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ultrametric networks: a new tool for phylogenetic analysis.
Apostolico A, Comin M, Dress A, Parida L.
Algorithms Mol Biol. 2013 Mar 5;8(1):7. doi: 10.1186/1748-7188-8-7.
:: DESCRIPTION
GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion. On a practical level, the program is able to perform maximum-likelihood tree searches on large data sets in a number of hours.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
rRNA phylogeny is a program package to phylogenetic analyses (using Phylip) of rRNA using a matrix of empirical substitution rates and the OTRNA model.
4to20 translates DNA/RNA sequences to rRNA-coded sequences in 20-letter code
20to4 translates rRNA-coded sequences to 4-letter code
nadist performs Distance analysis using the OTRNA model and gamma-distributed rates.
rRNAdist, rRNAml, rnaml: modified versions of protdist, protml, protmlk from PHYLIP to use the rRNA matrices.
etseqgen: modification of PSeq-gen to use the PMB model or the Bacterial SSU rRNA model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Empirical substitution models for Ribosomal RNA
Andrew Smith, Thomas W. H. Lui and Elisabeth R. M. Tillier,
Mol Biol Evol (2004) 21: 419-427
High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA
Tillier, E. R. M. and R. A. Collins,
Genetics (1998) 148: 1993-2002
:: DESCRIPTION
BYPASSR is the implementation of a new method for inferring branch lengths and site-specific substitution rates from nucleotide sequences. It makes use of the Bayesian Markov Chain Monte Carlo method and of the uniformization (randomization) technique to calculate sequence substitution probabilities in complicated DNA substitution models such as general time reversible model (GTR).
BYPASSRdegr is a software packages for estimating degradation levels of ancient DNA sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Syst Biol. 2006 Apr;55(2):259-69.
Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation.
Mateiu L, Rannala B.
Bayesian inference of errors in ancient DNA caused by postmortem degradation.
Mateiu LM, Rannala BH.
Mol Biol Evol. 2008 Jul;25(7):1503-11.
:: DESCRIPTION
DISPAN (Genetic Distance and Phylogenetic Analysis) computes (1) average heterozygosity and its standard error for each population, (2) gene diversity (Ht) and its associate parameters, Hs, and Gst (Nei 1973), (3) standard genetic distances (D) between populations (Nei 1972), (4) standard errors of standard genetic distances (Nei 1978), (5) DA distances between populations (Nei et al. 1983). It also constructs phylogenetic trees by using the neighbor-joining (NJ) method (Saitou and Nei 1987) and the unweighted pair group-method with arithmetic mean (UPGMA) (Sneath and Sokal 1973) from matrices of either D or DA distances. Bootstrap tests (Efron 1982, Felsenstein 1985) for these trees can be performed
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RESTDATA computes (1) the numbers of nucleotide substitutions per site for pairs of DNA sequences and their standard errors (Nei and Tajima 1983) for the restriction site data, and (2) for the restriction fragment data estimates the numbers of nucleotide substitutions per site for pairs of DNA sequences (Nei and Li 1979). It also constructs phylogenetic trees (dendrograms) by using the neighbor-joining (NJ) method (Saitou and Nei 1987) and the unweighted pair group method with arithmetic mean (UPGMA) (Sneath and Sokal 1973) from estimates of the numbers of nucleotide substitutions. Bootstrap tests (Efron 1982, Felsenstein 1985) for these trees can be performed by resampling restriction enzymes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MacClade is a computer program for phylogenetic analysis. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
::DEVELOPER
David Maddison and Wayne Maddison
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Interactive analysis of phylogeny and character evolution using the computer program MacClade.
Maddison WP, Maddison DR.
Folia Primatol (Basel). 1989;53(1-4):190-202.
:: DESCRIPTION
XplorSeq facilitates the management of nucleic acid sequences for phylogenetic analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Frank DN (2008)
XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.
BMC Bioinformatics 9: 420.
:: DESCRIPTION
MPI-PHYLIP is a modified PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time.
::DEVELOPER
National Resource for Biomedical Supercomputing
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ropelewski AJ, Nicholas HB Jr, Gonzalez Mendez RR (2010)
MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families.
PLoS ONE 5(11): e13999. doi:10.1371/journal.pone.0013999
