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Matches2Distances command line options


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

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

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

Character coverage of the smallest genome

Breakpoint counting

Random distance matrix

Greedy with trimming with locus length correction

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)

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

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

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).

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

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

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

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.

Each accession id will be treated as an individual species.

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