IMEG Lab - Software

Phylogenetic Analysis

Converge by J. Zhang (readme file)
Designed to test convergent and parallel evolution at the amino acid sequence level. It computes the probabilities that the observed convergent and parallel substitutions are attributable to random chance.

Gamma by J. Zhang (readme file)
It estimates the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

LINTREE by N. Takezaki:
The programs on this page are for: (1) constructing a phylogenetic tree by using the neighbor-joining method; (2) testing the molecular clock on a given topology of a phylogenetic tree; (3) making linearized trees by reestimating branch lengths under the assumption of constant rate of evolutions.

for DOS - LINTREE (readme file)
for UNIX - LINTREE (readme file)

METREE by A. Rzhetsky (readme file)
Program that computes minimum evolution (ME) trees from DNA and amino acid sequence data and tests the statistical significance of topological differences and of the branch lengths of those tree. This method is incorporated in MEGA and MEGA2.

Phyltest by S. Kumar (readme file)
Program for (1) four-cluster analysis, (2) interior-branch test, (3) relative rate tests and the computation of the time of divergence and (4) estimation of average pairwise distances (and standard errors) within and between clusters of sequences.

Statio by Andrey Rzhetsky
Program for testing stationarity of nucleotide and amino acid composition in a set of sequences, as described here.

TIMER by G. Glazko (readme file)
It estimates the divergence times using linearized-tree approach. Compared with the program LINTREE (Takezaki et al. 1995), TIMER has more user-friendly interface. More importantly, TIMER can be used to estmate divergence times for concatenated or very large set of genes (proteins).

Ancestral Sequences

Ancestor by J. Zhang (readme file)
Program which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known.

Anc-gene by J. Zhang (readme file)
Program for inference of ancestral nucleotide sequences of protein coding genes from a set of present-day sequences whose phylogenetic relationships are known. It first infers the amino acids by the distance-based Bayesian method, and then infers the underlying nucleotide sequences by fixing the inferred amino acids.

Phylogenetic Test of Adaptive Evolution

ADAPTSITE by Y.Suzuki (readme file)
The original program which implements the Suzuki and Gojobori's (1999) method of detecting positive and negative selection at single codon sites.

Bn-Bs by J. Zhang (readme file)
Program to estimate branch lengths in terms of synonymous and nonsynonymous substitutions per site, while the tree topology is given. The program uses the modified Nei-Gojobori method (Zhang et al. 1998) to estimate pairwise synonymous and nonsynonymous distances among present-sequences and then estimates branch lengths and their variances by using the ordinary least-squares method.

Fisher by J. Zhang (readme file)

HON-new by J. Zhang (readme file)
This program estimates conservative and radical nonsynonymous distances between protein coding DNA sequences. The method is modified from the original method of Hughes, Ota, and Nei (1990) by taking into account the transition bias. Three types of amino acid classifications (charge, polarity and that of Miyata and Yasunaga) are provided. One can also define conservative and radical amino acid changes by oneself.

NG-new by J. Zhang (readme file)
It implements the modified Nei-Gojobori method of estimating synonymous and nonsynonymous distances between protein coding DNA sequences (takes into account the transition bias). The original Nei-Gojobori method and several other methods, including NG-new method, are included in MEGA2.

SEND by L. Jin (readme file)
Program for computing the standard errors of the average number of nucleotide substitutions per site within and between populations.

SENDBS by N. Takezaki (readme file)
This program computes average nucleotide substitutions within and between populations with standard errors of average nucleotide substitutions estimated with a bootstrap method by resampling sites. Also constructs a population tree with a neighbor-joining method.

SGI by C.Su (readme file)
Program implements the Suzuki and Gojobori's (1999) method of detecting positive and negative selection at single codon sites (PC version).

Restriction Enzyme

RESTDATA by T. Ota (readme file)
This program 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.

RESTSITE by J. Miller (readme file)
It computes distances between species based on restriction sites or restriction fragments and can infer phylogenies by the Neighbor-Joining and UPGMA distance matrix methods.

SEND by L. Jin (readme file)
Program for computing the standard errors of the average number of nucleotide substitutions per site within and between populations.

Population Trees from Genetic Markers

DISPAN by T. Ota (readme file)
This program 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.

POPTREE (formerly NJBAFD) by N. Takezaki:
You can (1) construct a neighbor-joining tree or a UPGMA tree from allele frequency data of microsatellite DNA loci or other genetic markers and (2) compute heterozygosities and Gst value.

for DOS - POPTREE-DOS (readme file)
for UNIX - POPTREE-UNIX (readme file)

Heterozygosities and Gst

Related Statistics

Fisher by J. Zhang (readme file)

Critical values of the Z-statistic

Reverse translation program

aa2dna by J. Nam
is designed to align cDNA sequences on the basis of protein alignment.

Functional differentiation

dde by J. Nam
for DOS - DDE-DOS
for UNIX - DDE-UNIX
is designed for predicting the functional differentiation of duplicate genes.