Partition strategy (+ alternative support methods)

[max maronna]

Hello Derrick and garli users

I have a datamatrix with two coding genes (defining each codon position in both cases), and I want to define first the best partition strategy (with PartitionFinder), and then run my phylogenetic inference in Garli.

PartitionFind gave me this (best) result:

-------------------------------------------------

Subset | Best Model | Subset Partitions | Subset Sites                            
1 | GTR+I+G | Gene1_pos1, Gene1_pos2, Gene2_pos3 | 1-172\3, 2-172\3, 175-855\3  
2 | TrN+I+G | Gene1_pos3, Gene2_pos2 | 3-172\3, 174-855\3
3 | TrN+I+G | Gene2_pos1| 173-855\3 

Scheme Description in PartitionFinder format
Scheme_step_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos3) (Gene1_pos3, Gene2_pos2) (Gene2_pos1);

RaxML-style partition definitions
DNA, p1 = 1-172\3, 2-172\3, 175-855\3
DNA, p2 = 3-172\3, 174-855\3
DNA, p3 = 173-855\3

-------------------------------------------------

My question is: Can Garli handle this partition strategy (in the .config file)? Or should I manually pick the different positions from each gene, and build a new datamatrix (considering PartitionFinder´s result, with 3 partitions).

My other question is: Any possibility to include new support methods in garli? Specially considering aBAYES, aLRT and SH-aLRT (from PhyML)...

Thanks in advance!

max

[Derrick Zwickl]

Hi Max,

No, Garli will currently only accept the specification of a partition scheme using a Nexus charpartition, as described here:
https://www.nescent.org/wg_garli/Using_partitioned_models
You certainly shouldn't need to extract your own new matrices.

I've thought about adding other measures of support, but don't have any immediate plans to do so.

Best,
Derrick

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