search

clifmckee / genotyping-review

Files from Kosoy et al (2018) Parasitology
0 stars 0 forks source link

what is the file "barcode_663R_4130C_MAFFT_GTR+G4+I_ML_branch.csv" used for next step? #3

Open liamxg opened 10 months ago

liamxg commented 10 months ago

@clifmckee

clifmckee commented 10 months ago

Those files are the phylogenetic distance matrix calculated for all the species/strains in the sequence alignment for that gene. This was the branch lengths between species based on a maximum likelihood tree. I'm not sure I used these in any of the figures, though. I think I used the Tamura-Nei distances that I calculated inside of the MEGA program for the values plotted in Figure 2.

liamxg commented 10 months ago

Thanks. First, Tamura-Nei distances is genetic distance or phylogenetic distance?

liamxg commented 10 months ago

Second, what is the different between the results from the command "cophenetic" and calculate the genetic distances in MEGA?