gene partition+codon position partition

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mohammadreza ashrafzadeh

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Nov 12, 2015, 5:21:29 AM11/12/15
to PartitionFinder

I have one mitochondrial protein-coding gene (full Cytochrome b, 1140bp) and one non-coding region (D-loop, 436bp). I'm trying to find the best partitioning scheme within the dataset, based on "gene partition+codon position partition".

How can define one data block for this dataset in PartitionFinder?

 

Which data block is correct?

1)

## ALIGNMENT FILE ##

alignment = allseq.phy;

## BRANCHLENGTHS: linked | unlinked ##

branchlengths = linked;

## MODELS OF EVOLUTION (e.g. GTR): all | raxml | mrbayes | <list> ##

models = all;

# MODEL SELECCTION: AIC | AICc | BIC #

model_selection = BIC;

## DATA BLOCKS: see manual for how to define ##

[data_blocks]

Gene1_codon1 = 1-1140\3;

Gene1_codon2 = 2-1140\3;

Gene1_codon3 = 3-1140\3;

Gene2 = 1141-1576;

## SCHEMES, search: all | user | greedy | rcluster | scluster ##

[schemes]

search = all;

 

 

or,

 

2)

## ALIGNMENT FILE ##

alignment = allseq.phy;

## BRANCHLENGTHS: linked | unlinked ##

branchlengths = linked;

## MODELS OF EVOLUTION (e.g. GTR): all | raxml | mrbayes | <list> ##

models = all;

# MODEL SELECCTION: AIC | AICc | BIC #

model_selection = BIC;

## DATA BLOCKS: see manual for how to define ##

[data_blocks]

Gene1  = 1-1140;

Gene1_codon1 = 1141-2280\3;

Gene1_codon2 = 1142-2280\3;

Gene1_codon3 = 1143-2280\3;

Gene2 = 2280-2716;

## SCHEMES, search: all | user | greedy | rcluster | scluster ##

[schemes]

search = all;

 

However, I have run PrtitionFinder for the first data block and resulted in the following best scheme:

Subset | Best Model | Subset Sites                                          

1          | K80               |  380                           

2          | HKY              | 380                           

3          | HKY              | 380                           

4         | K80+I+G       | 436    


Thanks in advance                     

Rob Lanfear

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Nov 12, 2015, 5:24:46 AM11/12/15
to PartitionFinder
Hello,

The first configuration file reflects what you described in your email, assuming that your coding gene comes first in your alignment file. 

Rob

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Rob Lanfear
School of Biological Sciences,
Macquarie University,
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