I have called SNPs in 280 genomes and have identified sites where at least 1 individual possesses an alternate allele to the reference genome. I then concatenated all of these sites together for each genome, resulting in sequences of roughly 650,000bp. I'm hoping to create a phylogenetic tree using Phylip and a Neighbour-Joining method, but I'm having trouble picking the most appropriate model of evolution.
Partition Finder and JModelTest - both excellent programs for deducing best fit models - appear to both expect triplet codons, and do not offer an obvious way to adapt them to cope well with concatenated SNPs from across a genome. I wonder if anyone has any suggestions of how I might use either of these programs, or an alternative solution? Specifically, would using Partition Finder's 'Data Blocks' option allow me to get past this issue (e.g. Charset = Start - End/1')?
Many thanks,
Ian
Concatenation methods have been criticized for creating inflated support values, and ignoring potentially multiple independent gene histories in your data... Thus it is possible to create apparently strong support for an "incorrect" topology, or misrepresent the support for a "correct" topology (insofar as there exists an ascertainable "correct" topology).
In addition to checking out SNAPP as already suggested, I would look into SVDQuartets, which runs MUCH faster than SNAPP. SNAPP (in my experience) can take months even on HPC for a large dataset.
Hi Ian,
Both PartitionFinder and jModelTest have no problems analyzing entire non-partitioned data sets. These programs only perform best-fit model selection for the partitions you specify beforehand. For PartitionFinder, you can specify a single partition in the Data Blocks that will include all sites in your sequence, e.g.:
Charset = 1 - 650000; // no need to divide it by 1
For jModelTest, you can just load your entire sequence file making sure to convert it into phylip format; then you can do model selection for the entire data set.
I would also suggest that you consider using SNAPP add-on for BEAST 2 software that's designed for that specific type of data.
Cheers,
Oksana
Hi Oksana,
Fantastic, thank you very much for explaining it all so clearly! I'll have a look at BEAST 2 and the SNAPP add-on now.
Cheers,
Ian
Concatenation methods have been criticized for creating inflated support values, and ignoring potentially multiple independent gene histories in your data... Thus it is possible to create apparently strong support for an "incorrect" topology, or misrepresent the support for a "correct" topology (insofar as there exists an ascertainable "correct" topology).
In addition to checking out SNAPP as already suggested, I would look into SVDQuartets, which runs MUCH faster than SNAPP. SNAPP (in my experience) can take months even on HPC for a large dataset.
Hello Ian,
I would also suggest you read the following paper about acquisition bias correction in inferring SNP phylogenies.
http://sysbio.oxfordjournals.org/content/early/2015/09/15/sysbio.syv053.long
Also I will point out that, while this is still a point of contention in the literature, using linked SNPs can lead to bias in the resulting phylogeny if there is gene discordance. Most species tree methods are made using unlinked SNPs and thus using highly linked SNPs can be problematic. Below is a good article that sums up some of these issues.
http://www.sciencedirect.com/science/article/pii/S1055790315003309
Best Regards
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