Re: Bali-Phy Question

[Benjamin Redelings]

Hi Ben,

BTW, would you mind sending questions to the google group, so that other
people can benefit from the answers?

1. I think you should probably use the alignment-max command instead of
the alignment-consensus command.

2. You can do something like this, using pipes:

cut-range --skip=1000 run-1/C1.P1.fastas run-2/C1.P1.fastas |
alignment-chop-internal -N 25 | alignment-max > p1-wpd.fasta

The cut-range command is almost like "cat", but it allows you to skip
the first (say) 1000 iterations.  The alignment-chop-internal command
removes internal sequences, but you have to specify the number of leaf
sequences to keep.

3. If you just run `bp-analyze run-1 run2`, you should get a nice
report.  It should include an alignment based on samples from both runs,
constructed using alignment-max.  If you look in Results/command.log, it
records the command that are run. However, with pipes, you might only
see the last command in the pipeline.

-BenRI