How to get the codon position correctly for setting data blocks

[nmooy]

Hello, 

　I am trying to set the data block in "partition_finder.cfg" for my protein coding sequence.

　Because of defining codon positions would directly influence the quality of phylogenetic trees, i was worried about setting it in a wrong way. Maybe someone could give me any advice, i'd be very appreciate.

　For alignment, i would aligning multiple sequences and cut extra nucleotide to made every sequences for the same length, than click on tab "translated to protein sequences" and export the data.

　if the sequence length was 1000, is it correct that i set

gene1_postion1 = 1-1000\3;

gene1_position2 = 2-1000\3;

gene1_position3 = 3-1000\3;

　or should i take the start codon and stop codon into consideration, then trim sequences in other way rather than making it same length.

[Rob Lanfear]

Hi there,

As long as your sequences all remain in frame along the entire alignment, your suggestion should work. 

The simplest case is if they are in frame 1, where the first position of the alignment is also the first codon position of the first amino acid in that alignment. This case agrees with the data blocks you’ve suggested in your example (where position1 starts at column 1). 

More generally, all you need to worry about is grouping all of the 1st codon positions into a single data block, the 2nd codon positions into another, and the 3rd codon positions into another. You don’t need special consideration for start and stop codons.

Let me know if any of this doesn’t make sense.

Rob

[nmooy]

Hi Rob, 

　It is nice to get your reply, your information help me with setting up data blocks and made me had confidence to accomplish the following program. Appreciate for all the help you gave in the text.

rob.l...@gmail.com 在 2021年11月25日 星期四下午4:25:54 [UTC+8] 的信中寫道：