Content-type: text/html Manpage of QUARTM

QUARTM

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NAME

QUARTM - quartett mapping to indentify the phylogenetic position of
a query sequence

SYNOPSIS

quartm [options] < inputfile > outputfile

DESCRIPTION

quartm implements a version of the quartett mapping technique [K. Nieselt-Struwe and A. von Haeseler, Mol. Biol. Evol 18: 1204-1219 (2001)] in which a query sequence is compared to three or four groups of homologous sequences in order to determine its phylogenetic position relative to these groups. It uses Ken Clarkson's code for computing the convex hull.

OPTIONS

-g: ignore all quadruples that contain a '-' (gap character).
-F<n>: use frame <n> of coding nucleic acid sequences. Note that there must not be frame-shifts in the input alignment!
-4: use only the first four input blocks (see below).
-v: verbose; printer a header specifying the options.
-h: print a usage message and exit.
-V: print version information and exit.

FILES

input: quartm uses a phylip-like alignment format in which each sequence MUST stand on a single line preceeded by a name or ID of the sequence. This name must not contain a whitespace (blank or tab character). The input file contains either 4 or 5 blocks of data. The sequences in the first block are used independently as query sequences. The data blocks are separated by lines of the form
& blockname
If four blocks are specified, the program uses blocks 2, 3, and 4 in combination with all query sequences. In the case of five blocks the query is compared to all six possibilities of combining two of the four reference groups.
output: The program prints the list of the sequence IDs in each input group. Then the mean support for each of the trees is listed together with the width of the distribution of support values. A graphical representation of the support values from each quadruple is plotted in Postscript. Filenames are automatically generated from the IDs of the query sequences and the reading frame, if applicable.

REFERENCES

K. Nieselt-Struwe and A. von Haeseler, Mol. Biol. Evol 18: 1204-1219 (2001)

VERSION

This man page documents version 0.2

AUTHOR

Peter F Stadler.

BUGS

The code is ugly because it consists of lots of distinct cases that are just different enough to make it non-trivial not to deal with them one-by-one. The program should probably (also) read a more standard input format.

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Time: 19:27:48 GMT, June 07, 2005