phyloscanner

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phyloscanner.analyse.trees.R

1

Hi, I'm getting the following error when I try to run phyloscanner_analyse_trees.R: Error in phyloscanner.analyse.trees(tree.directory, tree.file.regex, reconstruction.mode, : could not find function "phyloscanner.analyse.trees" Any suggestions? Thanks! Amanda

amcasto

phyloscanner_analyse_trees.R problem

4

Hi, I have been running into the same problem with both my own data set and the example dataset provided. For the example dataset my code is identical to that...

KF-DR

Bam file has more than one references given

3

Hello. Running the EstimateReadcountperwindow.py python script but the resulting error was that the first bam file had more than one references given and it just expected one. Any assistance will...

simeonhebrew

Bootstrapping trees 1st part

3

Hello developers. I am trying to use this software am interested in how the bootstrapping procedure works for making the trees? When you specify the number of bootstraps it seems...

evandiego83

- functions to reconstruct tranmission networks (this is the old pull request that I believe) - functions to convert to SIMMAP trees, and back - vignettes

olli0601

Make the consensus files an option

1

(and update the manual)

ChrisHIV

Some potential tree input (e.g. RAxML bootstraps) have no branch lengths. At present phyloscannerR cannot deal with these. The easiest solution is to give them arbitrary lengths and warn the...

mdhall272

pysam's "is_duplicate" attribute

ChrisHIV

Try to wrap together the --x-raxml args with quotation marks.

ChrisHIV

RAxML failing without error message

5

Hi, I have a issue. I have up to date version. I just try to follow the example. I installed VirtualBox on my computer and ran Ubuntu 16.04.3. But on...

ChrisHIV