Options:

Matches2Distances Version 0.99r
$Id: Matches2Distances.java,v 1.44 2008-04-06 15:38:23 aauch Exp $

Usage: Matches2Distances [options ...] files_length files_data -out(p|n) outfile

Options:
-greedy, -greedy2
Selects between Greedy and Greedy with trimming.
If omitted, no filter is used
-coverage
Character coverage filtering

-coveragemin
Character coverage of the smallest genome

-breakpoint
Breakpoint counting

-random
Random distance matrix

-localGreedy
Greedy with trimming with locus length correction

-localGreedy2
Greedy with trimming with extended locus length correction

-matrixN, -matrixU, -matrixL, -matrixA
N gets the matrix without modifications
U gets the upper matrix copied to the lower values
L gets the lower matrix copied to the upper values
A calculates the average between upper and lower values
-matrixMin, -matrixMax
returns only the minima or rather the maxima in the matrix

-sort[L|I|S|E ...] (only important if greedy or greedy2 selected)
Sort by length of hits (default), by Identity value, by score or by e-value
Example: -sortSLI sorts by score, length and at last by Identity

-scale <double factor>
Multiplies matrix values with <factor>.
This can be used for phylip output to extend the precision (phylip uses only
5 digits after the decimal point)

-outp filename, -outn filename
Writes output in Phylip or Nexus format (both can be selected)

-nexus-short
For Nexus-Output only. Writes Genebank-IDs as Taxa. Default is full
bacteria name

-nofnid
Affects how the erg-Files are mapped to the corresponding Genomes.
Default is to use the Filename. With this option enabled the Description-Tag of the DATA-Header is used instead.

-replaceFactor <factor>
When a value of positive infinity is found in the matrix,
it is replaced by the highest value multiplied with this factor.
Default: 1.5

-blastTabular
files_data will be interpreted as a single blast input file in
tabular format (-m 9)

-replaceTable <filename>
Specifies a file listing replacement strings for taxa names.
Each line includes a search string (regexp) and the replacement string
separated by a single colon.

-eValueThreshold <long threshold>
logarithmized threshold for eValues (eg. -10 for eValues <= 10e-10).

-noRepairNV
do not repair negative distance values any more (replaced with 0 otherwise)

-repairZ
repair zero distance values (replaced with maxVal*const
otherwise, see replaceFactor)

-j <int jobCount>
specifies the number of jobs to run simultaneously

-nexus-LongAccession
Writes full bacteria name plus its accession No. as taxa labels

-errorDistanceValue <double distValue>
Instead of exiting when an error occurs in the distance functions, return this
value in the matrix.

-errorNoDataValue <double distValue>
Instead of exiting when no data is present at all, return a matrix
having each entry replaced with the given value.

-minGenomeSize <long>
Sets the minimal genome size used as divisor in the distance functions.

-multiChromosomesOff
Each accession id will be treated as an individual species.