[Biopython-dev] Parsing PAML supplementary output

[Peter Cock]

On Tue, Oct 11, 2011 at 10:33 AM, Brandon Invergo <b.invergo at gmail.com> wrote:
>> Do we need to write the "I" flag in our PHYLIP output?
>
> It took me a while to hunt down information on PHYLIP flags. I found
> this link which mentions them:
> http://www.no.embnet.org/phylipdoc/
> They're only used by the program which is using the alignment as input,
> corresponding to the PHYLIP programs' menu options. In general, they
> have no affect on the format of the alignment (aside from the
> 'S'/sequential vs 'I'/interleaved flags). However, some of them might
> require extra information immediately below the header line, before the
> alignment starts. This complicates things. (see below for some PAML
> examples)

Some of those examples don't really look like PHYLIP anymore to me.

If there is any simple change to allow the current parser to cope
with (but ignore) any extra meta data like this, that sounds sensible
(with unit tests of course - grin).

Peter