#14 loss of first line of alignment in pipeline NEXUS output

[Mikhail Bezruchko]

Cross-references:
Date: 10/21/04
Submitted by: Arlin
Submitted to:
Status (open/fixed): open

In his 20 Septmeber email, Nick writes:

"I have also identified a bug in the alignment program which results in the
apparent deletion of the first line of the alignment in output NEXUS files.
This affects the alignment quality scores and the bayesian trees. The
alignment data and NJ trees are unaffected by this problem. Since this is
not my code, I had to write a new program to deal with the issue. This is
almost complete. I expect to have the corrected alignment quality scores for
the smaller protein families later this week. Fortunately I have found a way
to access the second processor on the Xserves which will double the
throughput."