Entering edit mode
2.7 years ago
sunnykevin97
▴
1000
HI,
Step 1- After performing MSA - Mafft and cleaning alignment using trimal.
Step 2-
I concatenated all the *.fa files into out.phy
, additionally generated partitions.txt
catfasta2phyml.pl *.fas > out.phy 2> partitions.txt
Total no. of partitions - 1080, does my partitions file is in the right format.
I don't know, exactly which model to be assigned. How do I choose the model for each partition ?
head partitions.txt
OG0015287.mt.r.fa = 1-431
OG0015288.mt.r.fa = 432-1222
OG0015290.mt.r.fa = 1223-1594
OG0015291.mt.r.fa = 1595-1724
OG0015292.mt.r.fa = 1725-2050
OG0015294.mt.r.fa = 2051-2215
OG0015295.mt.r.fa = 2216-2629
OG0015296.mt.r.fa = 2630-2984
OG0015298.mt.r.fa = 2985-3441
OG0015299.mt.r.fa = 3442-4362
OG0015300.mt.r.fa = 4363-4729
OG0015301.mt.r.fa = 4730-4841
OG0015303.mt.r.fa = 4842-5597
I ran the iqtree2 with out
providing partitions.txt
The iqtree2.log
file, says "9 sequences failed"
66959 parsimony-informative, 58943 singleton sites, 675786 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 0.000985321 secs using 99.66% CPU
1 A.v 12.30% failed 0.00%
2 C.l 1.25% failed 0.00%
3 E.d 17.75% failed 0.00%
4 E.s 31.46% failed 0.00%
5 L.f 20.00% failed 0.00%
6 L.g 20.18% failed 0.00%
7 L.li 22.04% failed 0.00%
8 L.t 4.30% failed 0.00%
9 P.a 7.02% failed 0.54%
10 P.s 2.50% `passed` 15.69%
**** TOTAL 13.88% 9 sequences failed composition chi2 test (p-value<5%; df=19)
NOTE: minimal branch length is reduced to 0.000000124737 for long alignment
Checking for duplicate sequences: done in 0.00445477 secs using 1716% CPU
Suggestions appreciated.