Running GARLI from our Model-O-Matic code.

If we remember from our model-o-matic output and sort by the lowest AIC, we can see the best model for OR6 is CodonM0.0.EQU+4dG. It is interesting how all codon models are preferred to the nucleotide models! This turned out to be the case in every set of alignments.

Things are looking good. I'll keep you posted on the results.

Here is the following best-fit models for each of the OR gene families (see summary files with AIC and likelihoods in /Volumes/Yango/Hayden_batORs/model_o_matic/excel_summaries):

OR137      CodonM0.0.EQU+4dG

OR213      CodonM0.0F64+4dG

OR4          CodonM0.0.F64+4dG

OR589      CodonM0.0.F64+4dG

OR6          CodonM0.0.EQU + 4dG

OR10        CodonM0.0.F64+4dG

OR11        CodonM0.0F64+4dG

OR51        CodonM0.0F64+4dG

OR52        CodonM0.0F64+4dG

Those highlighted in pink were run in model-O-matic as the -100normal parameter, as the program would crash if it was run as -normal. My thoughts are there are too many taxa, but other than than that I am at a loss.

Now we can apply this model to GARLI using our tree output. There are two options for running GARLI (at least that I use). One is on the CIPRES server, the other can be from command line. I am currently having CPU usage problems on CIPRES so I am going to run it from command.

Installing GARLI is easy if you have homebrew.

105-238:~ loloyohe$ brew install garli

Should be ready to go.

Let's take a second to interpret the output from

105-238:OR6 loloyohe$ garli garli.conf

Running GARLI Version 2.01.1067 (18 May 2012)

->Single processor version for 64-bit OS<-

##############################################################

 This is GARLI 2.0, the first "official" release including 

          partitioned models.  It is a merging of

   official release 1.0 and beta version GARLI-PART 0.97

  Briefly, it includes models for nucleotides, amino acids,

 codons, and morphology-like characters, any of which can be 

  mixed together and applied to different subsets of data.

    General program usage is extensively documented here:

            http://www.nescent.org/wg/garli/

      see this page for details on partitioned usage:

  http://www.nescent.org/wg/garli/Partition_testing_version

   and this page for details on Mkv mophology model usage:

    http://www.nescent.org/wg/garli/Mkv_morphology_model

         PLEASE LET ME KNOW OF ANY PROBLEMS AT:

                garli.support@gmail.com

##############################################################

Compiled Apr 27 2015 16:06:23 using GNU gcc compiler version 4.9.2

Using NCL version 2.1.17

#######################################################

Reading config file garli.conf

###################################################

READING OF DATA

Attempting to read data file in Nexus format (using NCL):

Phyllos_OR6_Funct_tAlign_noStops.nex ...

Reading DATA block...storing implied block: TAXA

storing read block: DATA

 successful

###################################################

PARTITIONING OF DATA AND MODELS

GARLI data subset 1

CHARACTERS block #1 ("Untitled DATA Block 1")

Data read as Nucleotide data,

modeled as Codon data

Gaps or ambiguity codes found within codon for taxon Lsi_29_OR6.

Codons coded as missing for that taxon: 6 120 235 236 

Gaps or ambiguity codes found within codon for taxon Phe_43_OR6.

Codons coded as missing for that taxon: 6 

Gaps or ambiguity codes found within codon for taxon Sti_17_OR6.

Codons coded as missing for that taxon: 185 

Summary of data:

  35 sequences.

  6 constant characters.

  232 parsimony-informative characters.

  5 uninformative variable characters.

  243 total characters.

  243 unique patterns in compressed data matrix.

Pattern processing required < 1 second

###################################################

NOTE: Unlike many programs, the amount of system memory that Garli will

use can be controlled by the user.

(This comes from the availablememory setting in the configuration file.

Availablememory should NOT be set to more than the actual amount of 

physical memory that your computer has installed)

For this dataset:

 Mem level availablememory setting

  great     >= 150 MB

  good approx 149 MB to 99 MB

  low approx 98 MB to 42 MB

  very low approx 42 MB to 31 MB

the minimum required availablememory is 31 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 224.4 MB of memory

**Your memory level is: great (you don't need to change anything)**

#######################################################

Found outgroup specification:  1

#######################################################

STARTING RUN

>>>Search rep 1 (of 2)<<<

MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)

Model 1

  Number of states = 61 (codon data, standard code)

  Nucleotide Relative Rate Matrix Assumed by Codon Model:     2 rates (transition and transversion) K param = 4.0000

  Equilibrium State Frequencies: equal (1/61 = 0.01639, fixed)

  Rate Heterogeneity Model:

    4 nonsynonymous rate categories, rate and proportion of each estimated

     (this is effectively the M3 model of PAML)

      dN/dS Proportion

      0.2500 0.2500

      0.5000 0.2500

      0.7500 0.2500

      1.0000 0.2500

Starting with seed=287687

creating likelihood stepwise addition starting tree...

number of taxa added:

 4  5  6  7  8  9  10  11  12  13  14  15  16  17

We can set the exact same thing up in CIPRES.