Construction of partial alignments

With this option you can select certain regions of the sequences in your input file and copy (save) them to a new file.  This can be interesting if you want to construct trees on the more conserved or more reliable areas of the alignment.  Remember that you can select these regions also in the process of ‘Distance estimation’.

If bootstrapping is needed on a part of the alignment, it is necessary to make a partial alignment first!

One of the options in the TREECON for Windows package is file conversion.  The main program that handles file conversion is the READSEQ program, written by D.G. Gilbert.  This program automatically recognizes different file formats, like PIR, NBRF, PHYLIP, OLSEN etc., and converts these to other formats.  It is now also possible to convert all these different formats (only alphabetical characters and ‘-’ are allowed in these files) into the TREECON input file format, and vice versa.  To change file formats, choose the option TOOLS from the TREECON main menu.  Since the implemented READSEQ program of Gilbert is not a Windows program, the screen will turn black for a while when TREECON calls this program.  Although annoying (a new file conversion program is being developed), this is not really a problem (just wait until the black screen dissapears), and after execution the Windows screen will reappear.  If the format conversion tool gives you any problems, try to copy the ‘readseq.exe’ file and the data(input)file to your working directory.

A new, versatile file conversion program for Windows is being developed (and finished, see below)!

With this option, it is possible to write the input file (in TREECON format, where the sequences are summed up one after the other) as a real alignment, written in blocks with a length specified by the user.  This can be useful to detect which parts of the sequence alignment is reliable and which is not.  This option can also be used if you want to publish part of the sequence alignment. It is also possible to write the alignment in one long block.  This can be interesting when you want to align a sequence manually with the other sequences of the input file.  Once the sequence is aligned, you can add the sequence with a normal word-processor to the original input file and start making trees.

TREECON can also indicate which positions of the alignment are phylogenetically informative in a maximum parsimony analysis.
 

In the current distribution of TREECON (since October 1998) the previous tools option in TREECON has been replaced by a completely new program called ForCon.  ForCon is a versatile windows software tool for the conversion of different alignment formats.  Furthermore, it is possible to make a selection of sequences and alignment regions to convert.