WAVES '0.1.0Beta' version, mind this is beta!

FastME - v2.1.4

Online since 8 Jun 2016, 5 p.m. / last update 12 Sep 2016, 3:42 p.m.


The input data file contains sequence alignment(s) or a distance matrix(ces).

Type of data in the input file. It can be either DNA or amino-acid MSA in PHYLIP format, or a distance matrix in PHYLIP format. If the input data type is a MSA, the menu will update to display evolutionary model options required to compute a distance matrix.

FastME implements a wide range of substitution models for DNA : p-distance, RY symmetric, RY, JC69, K2P, F81, F84, TN93, LogDet. F84 is the default option and is recommended in most cases.

FastME implements a wide range of substitution models for proteins : p-distance, F81-like, LG, WAG, JTT, Dayhoff, DCMut, CpREV, MtREV, RtREV, HIVb, HIVw and FLU. LG is the default option and is recommended in most cases.

Rates of evolution often vary from site to site. This heterogeneity is modelled using a gamma distribution.

Use this option to do [NNI] tree topology improvement.
You may choose the [NNI] type from: NNI_BalME or NNI_OLS

FastME may use an existing topology available in the input user tree file which corresponds to the input dataset.


Downloads

Archive (.zip) containing : - 20 input alignments used to compare distance methods (NJ, NJ+OLSME, BioNJ, NJ+NNI, NJ+SPR, NJ+SPR-?, FastTree1) - 140 inferred trees and corresponding log-likelihoods - 1 resuming sheet (.xls and .ods)