Sequence Data

The 'Load Sequence Data' dialog window can be reached by selecting 'File ... Load ... Allele Sequences' from the main menu.   Here you have a choice of entering data for single-locus sequence file conversion or for multi-locus analysis.  By default, the multi-locus option is selected.

sequence load dialog

Sequence files must be in the FASTA format, and for supported species, these may be downloaded from the MLST web-site (http://pubmlst.org) .  FASTA files should contain no spaces within the sequences.  The alleles must be in sequential order.  The program does not read individual allele names but takes the first sequence to be allele 1, the second to be allele 2 and so on.  If this is not the case, analyses may be invalid.

Multi-locus

In order for most multi-locus analyses to be performed, sequence files containing alleles for each locus must be loaded.   In order to do this, the locations of these files need to be entered.   This is done by highlighting the locus name in the left-hand 'File Location' list and clicking 'Browse'.  A file load dialog will then appear and the sequence file can be located.  Continue until all the sequence file locations have been entered.  The full path of the files is displayed in the right-hand 'File Location' list.  If the path is longer than the window can display, ToolTip text will display the full path when the mouse is positioned over the truncated path.  File locations are saved to a configuration file so you should only have to do this once.  Once all the files have been located, click 'Load'.  Provided no errors are encountered, the sequence files will be loaded and certain analyses that require them will become enabled.

Single-locus

Single-locus sequence files may also be loaded in order to output the sequences in other formats - presently MEGA and NEXUS.    The file location may be entered by clicking 'Browse' and searching.  It is also necessary to enter the locus name in the appropriate text box.