Input tree

[fanhuan]

Hi Deren,

I was trying to provide user defined input tree but it does not work (got stuck there without any error messages). Could you please try and see whether you can reproduce the problem? Thanks!

The tree I used is a random 30 species ultrametric one (sp30.tre):
((((t3:0.03546664747,t10:0.03546664747):0.03542769548,((((t20:0.01022248237,t14:0.01022248237):0.006643977943,(t17:0.01408948611,t8:0.014089
48611):0.002776974204):0.01860290103,t16:0.03546936135):0.02307928936,(((t5:0.01379999717,t25:0.01379999717):0.01338132237,t24:0.02718131954
):0.01981542818,(t19:0.01829421996,t18:0.01829421996):0.02870252776):0.01155190299):0.01234569224):0.009261864559,(t1:0.04826562616,(t13:0.0
2627695183,t15:0.02627695183):0.02198867433):0.03189058135):0.01984379249,(((t28:0.04598097632,((t22:0.01661648246,t11:0.01661648246):0.0250
1832827,((t21:0.0196005595,(t26:0.008929907245,t7:0.008929907245):0.01067065225):0.007131581783,((t4:0.006193304346,t9:0.006193304346):0.010
45860409,t2:0.01665190844):0.01008023284):0.01490266944):0.004346165601):0.006363314203,t23:0.05234429053):0.01214267362,((t12:0.03181285344
,((t27:0.01327667385,t6:0.01327667385):0.003038107994,t29:0.01631478184):0.0154980716):0.01010201049,t30:0.04191486393):0.02257210022):0.035
51303585);

The command I used is:
simrrls -o test -L 1 -t sp30.tre -dm 1 -ds 0

Cheers,
Huan

[fanhuan]

I just down-graded to version 0.0.9 and it works with this tree! I hope this helps with the issue.

[dereneaton]

I see, it seems to hang and run forever. I'll try to fix the problem. Thanks.

[dereneaton]

The problem appears to be fixed. It was a problem with generating enough barcodes that had 2 base differences when you have enough taxa. I increased the barcode length.

[fanhuan]

Hi Deren, Is there a way to cite simrrls? Cheers, Huan On Aug 7, 2016, at 8:32 PM, Deren Eaton <[email protected]<mailto:[email protected]>> wrote: Closed #6<#6>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#6 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AG1e5yvlavu3wqlGFFUfVwQyblhy4QuYks5qdocjgaJpZM4JXgdQ>.

[dereneaton]

We first describe simrrls in the paper below which is still In Press. https://academic.oup.com/sysbio/article-abstract/doi/10.1093/sysbio/syw092/2682283/Misconceptions-on-Missing-Data-in-RAD-seq?redirectedFrom=fulltext Or, you could cite the github repo directly. I do not plan to publish a paper specifically about simrrls, so I would recommend either of the first two options. I'm glad to hear you're using it!

…

-Deren

On Mon, Feb 13, 2017 at 5:27 PM, Huan Fan ***@***.***> wrote: Hi Deren, Is there a way to cite simrrls? Cheers, Huan On Aug 7, 2016, at 8:32 PM, Deren Eaton ***@***.***<mailto: ***@***.***>> wrote: Closed #6<#6>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://github.com/ dereneaton/simrrls#6#event-747834982>, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AG1e5yvlavu3wqlGFFUfVwQyblhy4QuYks5qdocjgaJpZM4JXgdQ>. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFJUGKu37lXJWjvIfl9B7LbUYzGPZ0iQks5rcNjkgaJpZM4JXgdQ> .

-- Deren A.R. Eaton Associate Research Scientist Yale University Assistant Professor (starting 2017) Columbia University Department of Ecology, Evolution, and Environmental Biology