use populations --phylip to build phylogenetic tree

[Andres Reyes]

I am trying to build a phylogenetic tree using the output I obtained after running ref_map.pl. I have 107 individuals which can be divided in 7 populations (based on where they were sampled). However, the phylip output sequence is for each population, and not individual. I was wondering if there is a way to build that phylogenetic tree including all my individuals, and not using the 7 populations each as a unit.

I saw a similar question asked before but I did not find an answer (https://groups.google.com/forum/#!searchin/stacks-users/populations$20phylip$20unit/stacks-users/J1zynZyVjM0/82Db1aX7V9MJ) 

Thanks,

Andres

[mathi]

Hi Andres,
just give each individual a unique population ID in the population map, then they will be treated separately. However, have a look at the -p and -r parameters, because their effect changes when you do that! Also, bear in mind that the phylip output from populations will not contain polymorphisms within each population but instead a "consensus", so you are likely to overestimate the genetic distances by excluding polymorphism within the units on your tree...
Also, the phylip does not contain full length RAD-loci but is basically a concatenated SNP matrix.
(Last time I checked - perhaps Julian changed these things in the meantime)

regards, Mathias

[Andres Reyes]

Thanks for the advice, Mathias! I'll give it a try

[Sean Ryan]

Following up on your post Mathias,

Do you know if there is an option to output a concatenated set of sequences for each population instead of the SNP matrix? I imagine the fasta file output could be used to do this, but if there is an option to do this that would be great.

Thanks,
Sean

[Julian Catchen]

Hi All,

There are a number of ways to output population level data in a phylip
file using the populations program:

--phylip: output nucleotides that are fixed-within, and variant among
populations in Phylip format for phylogenetic tree
construction.

--phylip_var: include variable sites in the phylip output encoded using
IUPAC notation.

--phylip_var_all: include all sequence as well as variable sites in the
phylip output encoded using IUPAC notation.

--fasta: output full sequence for each unique haplotype, from each
sample locus in FASTA format, regardless of plausibility.

--fasta_strict: output full sequence for each haplotype, from each
sample locus in FASTA format, only for biologically
plausible loci.

Best,

julian

mathi wrote:
> Hi Andres,
> just give each individual a unique population ID in the population map,
> then they will be treated separately. However, have a look at the -p and
> -r parameters, because their effect changes when you do that! Also, bear
> in mind that the phylip output from populations will not contain
> polymorphisms within each population but instead a "consensus", so you
> are likely to overestimate the genetic distances by excluding
> polymorphism within the units on your tree...
> Also, the phylip does not contain full length RAD-loci but is basically
> a concatenated SNP matrix.
> (Last time I checked - perhaps Julian changed these things in the meantime)
>
> regards, Mathias
>
> Am Donnerstag, 12. Februar 2015 22:48:08 UTC+1 schrieb Andres Reyes:
>
> I am trying to build a phylogenetic tree using the output I obtained

> after running ref_map.pl <http://ref_map.pl>. I have 107 individuals