Anyone can help me to interpret this ClonalFrameML output?
Hi! I have executed the ClonalFrameML software for a tree with different species of the Mycobacterium genus.
However the output is not explained and I don't know if with this results I can trust my tree or what should I do (for example continue my analysis with the reconstructed tree).
Can anyone help me?
Thanks!
I paste here the importation_status.txt file:
Node Beg End
A.subflavus_prokka.gff 4767 4982
A.subflavus_prokka.gff 6678 6933
A.subflavus_prokka.gff 7374 7716
abscessus_prokka.gff 1 8025
avium_prokka.gff 1 8025
canettii_prokka.gff 1605 1959
chitae_prokka.gff 1 8025
confluentis_prokka.gff 1 8025
fallax_prokka.gff 1 8025
fortuitum_prokka.gff 1 8025
gilvum_prokka.gff 1 7623
kansasii_prokka.gff 1 8025
leprae_prokka.gff 1 8025
rutilum_prokka.gff 1 8025
smegmatis_prokka.gff 6690 6885
smegmatis_prokka.gff 7479 7689
vanbaalenii_prokka.gff 1 8025
NODE_21 1 615
NODE_22 1 8025
NODE_23 1 498
NODE_23 840 2896
NODE_23 3885 4728
NODE_23 5193 6420
NODE_23 7869 8025
NODE_26 1 8025
NODE_27 1 1023
NODE_27 2568 8025
NODE_28 1 8025
NODE_29 1 8025
NODE_30 1 510
NODE_30 1146 4987
NODE_30 5475 8025
NODE_31 1 1152
NODE_31 2154 2931
NODE_31 3495 3842
NODE_31 4377 5023
NODE_31 5472 7488
NODE_32 2084 2640
NODE_32 4171 4185
NODE_32 5464 5510
NODE_32 7848 8025
NODE_33 1914 2021
NODE_33 6066 6556
NODE_33 7896 8025
NODE_34 1 8025
NODE_35 2350 2517
NODE_35 6098 6297
NODE_36 2449 2534
NODE_36 6045 6519
NODE_37 1 564
NODE_37 1395 2928
NODE_37 3378 6831
NODE_37 7551 8025
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Have you looked at the plots you can produce from the output? These will probably help you understand the output.
It's been a while since I used it, but IIRC, that file tells you the intervals of sequence which are likely horizontally acquired.
Yes, the plot that produces is this one. As I know: Blue horizontal lines are recombination events identified by ClonalFrameML. Short vertical lines are substitutions, non-homoplasies in white, homoplasies in yellow-red (increasing number of homoplasies at that site).
But that means that some species are totally recombination events in my tree? Do you know if I can trust my tree? How would you present this in a paper?
If you look, more or less all of the full blue lines correspond to some deep inferred node (i.e. I think this is essentially trying to do some ancestor reconstruction). I probably wouldn't pay a great deal of attention to this, and maybe focus on the clearer signal; e.g. in the top right you have a region between about 155000 and 180000 which looks to have quite a clear recombination signal.
This isn't really my area of major expertise, but I would perhaps look at some other papers that used CFML and look at what they've done and been able to infer.
Hi There How did you use importation_status.txt output in tree? Is there any command or R script for this?
There is an R script included with CFML to create the plots above from that file