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FastTree crashes if input topology tree has polytomies

Status: Open.

#32 In tnngh/Umberjack;

· tnguyencfe opened on Mar 29, 2016

Rooted tree in subs/time units is being passed to HyPhy for ancestral reconstruction instead of tree in subs/site

Status: Open.

#31 In tnngh/Umberjack;

· tnguyencfe opened on Jan 30, 2016

Do not squelch logging config file

Status: Open.

#30 In tnngh/Umberjack;

· tnguyencfe opened on Dec 3, 2015

Document required glibc for test simulation packaged binaries

Status: Open.

#29 In tnngh/Umberjack;

· tnguyencfe opened on Nov 25, 2015

Replace indelible binary that comes packaged for simulations with version compiled with older GLIBCXX

Status: Open.

#28 In tnngh/Umberjack;

· tnguyencfe opened on Nov 25, 2015

Consensus.add_seq() appending extra pad characters when the rightmost codon has no pad characters

Status: Open.

#27 In tnngh/Umberjack;

· tnguyencfe opened on Nov 18, 2015

MPIPool should have a terminate() method which ensures that no new work is accepted

Status: Open.

#26 In tnngh/Umberjack;

· tnguyencfe opened on Nov 18, 2015

Check if there are multiple timepoints before timing with RootToTip

Status: Open.

#25 In tnngh/Umberjack;

· tnguyencfe opened on Nov 17, 2015

Remove duplicates in input msa fastas

Status: Open.

#24 In tnngh/Umberjack;

· tnguyencfe opened on Nov 17, 2015

Read in .bam files

Status: Open.

#23 In tnngh/Umberjack;

· tnguyencfe opened on Nov 17, 2015

Use CSV file to specify input sams/msa fastas and their output files

Status: Open.

#22 In tnngh/Umberjack;

· tnguyencfe opened on Nov 17, 2015

Use FastTree packaged with Umberjack as default

Status: Open.

#21 In tnngh/Umberjack;

· tnguyencfe opened on Nov 17, 2015