[Biopython-dev] [Biopython] Phylogenetic trees with biopython?

[Peter]

On Mon, Sep 7, 2009 at 11:54 PM, David Winter<david.winter at gmail.com> wrote:
> Hi Peter and all,
>
> Sorry the lack of communication from me on this. I successfully made it off
> the grid for the weekend then found I couldn't push to github from work (no
> ssh over the proxy for students) and couldn't email the list from home
> (can't use the uni's SMTP from off campus ) - IT-security catch 22!

Tricky.

>> I see you've switched to _EmbossCommandLine - fine.
>
> Yeah, this was my stupid fault - you'd given me a heads up about the two
> different version of the _EmbossCommandline and I tried out what I already
> had with the the 'normal' version as saw that it failed but didn't read the
> error message properly (of course it failed because I was trying to give it
> the outfile parameter twice...)

OK - I wondered if there was some other reason I couldn't see, so worth
checking,

>> I have checked this into CVS, but did also fix an old typo (in a
>> docstring) and one new typo (in an argument name). Thanks David!
>>
>> Do you fancy writing a short unit tests? e.g. test_Emboss_phylip.py
>> based on test_Emboss.py? Continuing on the github branch is fine.
>
> Sounds good, will have a go at getting something going in the next
> couple of days

Great - whenever you get time. Thanks!

>> We should put you in the CONTRIB file now too (are there any other
>> recent people we've missed?). Would you like to give a webpage, or
>> is this email address fine (be warned it may get harvested for spam)?
>
> Well, I'm not sure it's much of a contribution from me, but thanks :)

But I'm expecting more in future *grin*

> Perhaps add david.winter at gmail.com - gmail seems to handle spam
> pretty well and I won't be a student here for ever (right?...)

There is always a postdoc ;)

Also can someone remind me at some point that we should include
at least one of the EMBOSS PHYLIP tools in the alignment command
line bit of the tutorial...

Peter