Branch lengths visualisation

[ldutoit]

Hi,

thank you for a fantastic software. I know this is talked about in the tutorial and in some issues but I just cannot seem to visualise branch lengths.

I inputted trees to Astral and then annotated the output tree as follow:

java -jar astral.5.7.4.jar -i ALLRAxML_bestTree.tre -o ALLTHEGF_bestTree.tre

#annotate each branch
java -jar astral.5.7.4.jar -q ALLTHEGF_bestTree.tre -i ALLRAxML_bestTree.tre -o Astral_Scores_test.tre -t 2

I obtained the following tree:

(A,(B,(C,((D,E)'[q1=0.6492709670753897;q2=0.17078776877555552;q3=0.17994126414898182;f1=48883.61111110609;f2=12858.611111111575;f3=13547.77777777684;pp1=1.0;pp2=0.0;pp3=0.0;QC=18;EN=75290.0]':0.642251644494381,((J,K)'[q1=0.8141459689201473;q2=0.07307012883516813;q3=0.11278390224464857;f1=61297.04999999789;f2=5501.449999999808;f3=8491.49999999959;pp1=1.0;pp2=0.0;pp3=0.0;QC=20;EN=75290.0]':1.2772704042843872,(I,(F,(G,H)'[q1=0.763622327002258;q2=0.14648525700624254;q3=0.08989241599149954;f1=57493.125;f2=11028.875;f3=6768.0;pp1=1.0;pp2=0.0;pp3=0.0;QC=8;EN=75290.0]':1.0368164294930535)'[q1=0.7495190027133111;q2=0.07991575432138566;q3=0.17056524296530742;f1=56431.28571428519;f2=6016.857142857126;f3=12841.857142857996;pp1=1.0;pp2=0.0;pp3=0.0;QC=14;EN=75290.0]':0.9788673697712466)'[q1=0.4727759330588509;q2=0.22122946827823983;q3=0.30599459866294726;f1=35595.30000000088;f2=16656.366666668677;f3=23038.3333333333;pp1=1.0;pp2=0.0;pp3=0.0;QC=30;EN=75290.0]':0.23465262815767224)'[q1=0.3715267631823497;q2=0.27663589675476813;q3=0.3518373400628786;f1=27972.249999999105;f2=20827.916666666493;f3=26489.83333333413;pp1=1.0;pp2=0.0;pp3=3.3430618804486773E-81;QC=48;EN=75290.0]':0.058988874772521314)'[q1=0.4203828529685242;q2=0.3360024571656051;q3=0.24361468986586746;f1=31650.625000000186;f2=25297.62499999841;f3=18341.75000000116;pp1=1.0;pp2=0.0;pp3=0.0;QC=24;EN=75290.0]':0.1399127436801601)'[q1=0.8231488245450923;q2=0.08465267631823616;q3=0.09219849913667154;f1=61974.875;f2=6373.5;f3=6941.625;pp1=1.0;pp2=0.0;pp3=0.0;QC=8;EN=75290.0]':1.3269197907699364));

But when trying to visualise it in FigTree I cannot seem to see the branch lengths:

I read again and again the tutorial and the issues but I cannot get my head around it and a tiny bit of help would be much appreciated!

Thank you

Ludo

[mobilegenome]

Hi Ludo,

if I remember correctly this is rather an issue with FigTree not being able to parse the Astral's Newick String correctly. For the sake of displaying the branch-lengths, you could try a) removing the the strings containing quartet scores ('[q1....]') before opening in FigTree or b) try a different visualisation tool.

Also remember that Astral, by design, is not estimating branch lengths for terminal branches.

Hope this helps

Fritjof

[ldutoit]

Thank you!

Indeed it seems to be a FigTree issue and https://itol.embl.de/ Deals with the tree just fine!

[smirarab]

Thanks Fritjof for the help. Ludovic, in FigTree, you need to click on "Branch labels" to see branch labels.

On Wed, Jan 27, 2021 at 3:14 PM Ludovic Dutoit notifications@github.com wrote:

Closed #71 https://github.com/smirarab/ASTRAL/issues/71.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/smirarab/ASTRAL/issues/71#event-4258383699, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGJXOCVKRXYXKWUWHKW7SDS4CM4VANCNFSM4WIFC5CQ .

-- Siavash Mirarab

[ldutoit]

Thanks!

That did not work for me or I did it poorly but the iTol worked just fine :)

Thank you for Astral and your answer!

Ludo