txtOutFilename.  and xmlOutFilename If you wish to specify a particular name for the output file, which you want to remain identical over several runs, you can set these two items to particular values. The default is to have the program select the output filename, which can be controlled by the next variable. [Default: not used]

outFilePrefixType . This option can either be omitted entirely (in which case the default will be filename) or be set in several ways. The default is set as filename, which will result in three output files named original-filename-minus-suffix-out.xml, original-filename-minus-suffix-out.txt, and original-filename-minus-suffix-filter.xml. [Default: filename]

If you set the value to date instead of filename, you'll get the date incorporated in the filename as follows: original-filename-minus-suffix-YYYY-nn-dd-HH-MM-SS-out.{xml,txt}. e.g., USAFEL-UchiTelle-2003-09-21-01-29-35-out.xml (where Y, n, d, H, M, S refer to year, month, day, hour, minute and second, respectively).

xslFilename. This option specifies where to find the XSLT file to use for transforming PyPop's xml output into human-readable form. Most users will not normally need to set this option, and the default is the system-installed text.xsl file.

fieldPairDesignator. This option allows you to override the coding for the headers for each pair of alleles at each locus; it must match the entry in the config file under validSampleFields and the entries in your population data file. If you want to use something other than _1 and _2, change this option, for instance, to use letters and parentheses, change it as follows: fieldPairDesignator=(a):(b) [Default: _1:_2]

popNameDesignator. There is a special designator to mark the population name field, which is usually the first field in the data block. [Default: +]

If you are analyzing data that contains a population name for each sample, then the first entry in your validSampleFields section should have a prefixed +, as below:

validSampleFields=+populat
 *a_1
 *a_2
 ...

validPopFields. If you are analyzing data with an initial two line population header block information as in Example 2.3, “Multi-locus allele-level HLA genotype data with sample and header information”, then you will need to set this option. In this case, it should contain the field names in the first line of the header information of your file. [Default: required when a population data-block is present in data file], e.g.:

validPopFields=labcode
 method
 ethnic
 country
 latit
 longit

permutationPrintFlag. Determines whether the likelihood ratio for each permutation will be logged to the XML output file, this is disabled by default. [Default: 0 (OFF)].

	Warning
	If this is enabled it can drastically increase the size of the output XML file on the order of the product of the number of possible pairwise comparisons and permutations. Machines with lower RAM and disk space may have difficulty coping with this.

arlequinExec. This option specifies where to find the Arlequin executable on your system. The default assumes it is on your system path. [Default: arlecore.exe]

markovChainStepsHW. Length of steps in the Markov chain [Default: 2500000].

markovChainDememorisationStepsHW. Number of steps of to “burn-in” the Markov chain before statistics are collected.[Default: 5000]

filtersToApply. Here you specify which filters you want applied to the data and the order in which you want them applied. Separate each filter name with a colon (:). Currently there are four predefined filter: AnthonyNolan, Sequence, DigitBinning, and CustomBinning. If you specify one or more of these filters, you will get the default behavior of the filter. If you wish to modify the default behavior, you should add a section with the same name as the specified filter(s). See next section for more on this. Please note that, while you are allowed to specify any ordering for the filters, some orderings may not make sense. For example, the ordering Sequence:AnthonyNolan would not make sense (because as far as PyPop is concerned, your alleles are now amino acid residues.) However, the reverse ordering, AnthonyNolan:Sequence, would be logical and perhaps even advisable.

alleleFileFormat. This options specifies which of the formats the Anthony Nolan allele data will be used. The option can be set to either txt (for the plain free text format) or msf (for the Multiple Sequence Format) [Default: msf]

directory. Specifies the path to the root of the sequence files. For txt: [Default: prefix/share/PyPop/anthonynolan/HIG-seq-pep-text/]. For msf files [Default: prefix/share/PyPop/anthonynolan/msf/].

preserve-ambiguous. The default behavior of the AnthonyNolan filter is to ignore allele ambiguity ("slash") notation. This notation, common in the literature, looks like: 010101/0102/010301. The default behavior will simply truncate this to 0101. If you want to preserve the notation, set the option to 1. This will result in a filtered allele "name" of 0101/0102/0103 in the above hypothetical example. [Default: 0].

preserve-unknown. The default behavior of the AnthonyNolan filter is to replace unknown alleles with the untypedAllele designator. If you want the filter to keep allele names it does not recognize, set the option to 1. [Default: 0].

preserve-lowres. This option is similar to preserve-unknown, but only applies to lowres alleles. If set to 1, PyPop will keep allele names that are shorter than the default allele name length, usually 4 digits long. But if the preserve-unknown flag is set, this one has no effect, because all unknown alleles are preserved. [Default: 0].

sequenceFileSuffix. Determines the files that will be examined in order to read in a sequence for each allele. (ie, if the file for locus A is A_prot.msf, the value would be _prot whereas if you wanted to use the nucleotide sequence files, you might use _nuc.) [Default: _prot].

directory. Specifies the path to the root of the sequence files, in the same manner as in the AnthonyNolan section, above.

binningDigits. An integer that specifies how many digits to keep after the truncation. [Default: 4].