No. 929

Title:

INTEROGATE 1.0: Exploration and testing of stationarity, reversibility and clock-likeness in sequence data

Author(s):

Waddell, Peter J.(Institute of Statistical Mathematics), Mine, Hiroshi(Institute of Statistical Mathematics), Patel, Amit(Department of Computer Science, University of South Carolina) and Hasegawa, Masami(Institute of Statistical Mathematics)

Key words:

Phylogenetic analysis; molecular sequence data; stationarity; reversibility; clock-likeliness

Abstract:

    INTEROGATE 1.0 is a set of C programs to facilitate the evaluation and editing of molecular sequence data. The package is intended to assist in phylogenetic analyses by giving the user important statistics on the data in conjunction with inferring an evolutionary tree. These statistics can assist in understanding which sites/models may be most suitable for analysis, and also which sequences may be significantly atypical. The user may then want to consider the results of analyses removing sites and/or particular sequences. Conversely, they can be used after inferring initial trees to ask what part, if any, of the tree may be incorrect. The programs are: Freqnuc, FreqAA and FreqCodon for analyzing the stationarity, reversibility and relative rate of nucleotide, amino acid and codon sequences, respectively; Capture, for estimating the proportion of invariant sites; Pcons, for assessing properties of constant sites; Exclcon, for removing constant sites from data; Perfect, for removing more rapidly evolving sites from the data or "site stripping"; Perfect2, for removing the same sites from matched amino acid and codon data.