[Biopython] More efficient neighbor joining algorithm to build phylogenetic tree

[Peter Cock]

On Tue, Aug 18, 2015 at 11:40 PM, Jing Lu <ajingnk at gmail.com> wrote:
> Peter Cock <p.j.a.cock <at> googlemail.com> writes:
>
>>
>> On Sat, Oct 19, 2013 at 4:16 PM, Jing Lu <ajingnk <at> gmail.com> wrote:
>> > Hello!
>> >
>> > I am trying to build a large tree (~10000 nodes) from a distance matrix
>> > by neighbor joining algorithm. I just modify the existing code from:
>> >
>> > https://github.com/lijax/biopython/blob/master/Bio/Phylo/TreeConstruction.py
>> > .
>> >
>>
>> Does it have to be in pure Python?
>>
>> Whenever I've needed a large tree with 1000s of sequences
>> I have used a fast C implementation, with bootstrapping.
>>
>> Peter
>>
>
> What is the implementation you use to build a large tree?
>
> Thanks,
> Jing

Hello again Jing,

I wonder if your email was stuck somewhere - or if you really are
returning to this project 2 years later?

I used to use Thomas Mailund's quick-join for large NJ trees:
http://users-birc.au.dk/mailund/quick-join.html

He now recommends RapidNJ instead:
http://birc.au.dk/Software/RapidNJ/

Both will accept distance matrices as input in PHYLIP format.

Peter