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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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Chromosome IDs #1

Closed peterdfields closed 10 years ago

peterdfields commented 10 years ago

Hi,

I'm trying to use SNPhylo but I'm running into some issues with the way the software expects only numbers for chromosome ID. The reference I'm using is still somewhat preliminary, and is composed of many many scaffolds, and scaffold is used in the naming nomenclature. I get the following with trying to run SNPhylo:

"Warning: There were 4396928 unreadable chromosome ids. Identifier for a chromosome should be a number."

Is it possible to bypass this particular requirement?

Thank you for your time and advice.

thlee commented 10 years ago

I am developing the new version of SNPhylo. Thus, please wait for a few weeks. Thanks.

thlee commented 10 years ago

I added new option to define the number of the autosomes. Thus, you can use SNP information determined with scaffolds. By the way, I think that the constraint that the chromosome number should be number is necessary to secure the integrity of data from the various chromosome ID formats. Thus, please change the scaffold IDs to numbers to use SNPhylo.

Thank you,