JLSteenwyk/orthosnap

only identify one SNAP-OG

XXboop opened this issue · 3 comments

XXboop commented

Dear Jacob
I used orthofinder for gene family clustering of five species (Ab, Ad, Ak, As, Lo). Then I would like to use orthoSNAP with default parameter to classify multi-copy gene families. But there are many gene families whose trees actually have multiple clades. But orthoSNAp can only identify one SNAP-OG. For example, the following gene families. orthoSNAP identified only one SNAP-OG, including Ab|AB06G03741-RB, Lo|LO08G03008-RA, As|AS05G03226-RB. But why wasn't the other clade identified as SNAP-OG？Can another clade be a SNAP-OG？

((Ab|AB06G03741-RB:0.0993161,(As|AS05G03226-RB:0.0364093,(Lo|LO08G03008-RA:0.0337749,Lo|LO08G03009-RA:0.0289553)0.996:0.0172954)0.992:0.0215731)1:0.0494888,((Lo|LO08G03007-RB:0.0387437,(As|AS05G03228-RB:0.0205169,As|AS05G03236-RA:0.0262063)0.897:0.0062029)1:0.157462,((Ad|AD03G00060-RA:0.0339494,(Ad|AD03G00059-RA:0.0129773,((Ad|AD08G00004-RA:0.0885369,Ad|AD08G00001-RC:5e-09)0:6e-09,Ad|AD08G00003-RA:0.0236448)0.763:0.00254957)0.632:0.00239112)0.912:0.0083526,(Ab|AB06G01323-RA:0.00687747,(Ab|AB06G01309-RA:0.00290853,Ak|AK09G04755-RB:0.00193846)0.734:0.0009175)0.991:0.0153459)1:0.267442)1:0.0494888);

image

Best regards
Xiaoxu

JLSteenwyk commented

Hi Xiaoxu,

I hope you are doing well.

You are only getting one SNAP-OG because the genes in the green box do not constitute a proper SNAP-OG. This is in part due to the relationship between the two Ab paralogs and Ak.

Hope this helps!

best,

Jacob

XXboop commented

Dear Jacob

Thank you for your reply. Is the clade in the green box not a SNAP-OG because Ab|AB06G01309 and Ak|AK09G04755 are clustered together,not Ab|AB06G01323. But bootstrap value of Ab|AB06G01309 and Ak|AK09G04755 is only 0.734? Can the clade in the green box become a SNAP-OG by adjusting orthosnap parameters? I did not change the results of orthoSNAP by adjusting the -s and -o.

best regards
Xiaoxu

JLSteenwyk commented

You can get two SNAP-OGs from that tree.

I would recommend changing the -s parameter from the default, which is 80, to something like 0.7.

Also, please make sure you are using the latest release, version 1.0.0.