Problem :

When you are working with different programs for phylogenetic research, you may have the problem that some programs use the complete species names (Treeconw), other will use the first 30 characters (Clustalw), and some will only use the first 10 characters (programs that work with Phylip files like Puzzle, fastDNAml, ...). For the final result, everybody wants a tree with complete names, but for most analyses, you have to shorten the names to 10 characters, and afterwards, you have to complete the names again. A lot of time is wasted that way, not mentioning the boring job to do this... Cutoff does this work for you... :-)

How does it work ?

Abbreviation of the names :

1. Cutoff reads the alignment file (PIR format) with the complete names.
2. If there is a space (' ') between the genus name and the species name, Cutoff replaces the space by an underscore ('_').
3. Cutoff uses the first 3 characters from the genus name, the first 3 characters from the species name and a increasing number of tree digits.
4. Cutoff writes an alignment file (PIR format) with abbreviated names, and a file (*.cof) with just the compete and the abbreviated names.

Caenorhabditis elegans 	--> Caenorhabditis_elegans	--> Cae_ele001
Globodera pallida	--> Globodera_pallida		--> Glo_pal002

Completion of the abbreviated names :

1. Cutoff reads a file (treefile, alignment, ...) with abbreviated names.
2. Cutoff reads the file (*.cof) with the complete and abbreviated names.
3. Cutoff replaces the abbreviated names with the complete ones (with the option to remove the underscores).
4. Cutoff writes an output file (treefile, alignment, ...) with the compete names.

Input format for abbreviation :

ONLY *.PIR format !! (accepts nucleotide (>DL;) or protein (>P1;) alignments.) The first line holds the species name. Cutoff is only using this line for abbreviation, all the other lines are copied identical to the output file.

example :

>DL;Caenorhabditis elegans
  length 10
ATGGTCCTGA*

or 

>DL;Caenorhabditis_elegans 
  length 10
ATGGTCCTGA*

Input format for completion of the names :

Cutoff accepts every text file. (I think...)

Installation :

Version history :

Cutoff 1.11 : minor update : removes empty lines from alignments while converting. (21-03-2000)

Cutoff 1.1 can read Dos/Windows and Unix/Linux files. (17-03-2000)

Cutoff 1.0 can only read Dos/Windows files. When using Unix/Linux files that were transferred with FTP as binary files to your Windows system, Cutoff 1.0 produced strange and unusable results. (Files that were transferred as ASCII did not cause any problems.)

Download :