BDI-pathogens phyloscanner issues

BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.

GNU General Public License v3.0

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issues

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Please consider providing an official Dockerfile and docker container for this tool

#80 Masterxilo opened 1 month ago
0
TypeError: object of type 'NoneType' has no len()

#79 MTDouglas opened 1 month ago
4
Docker/Singularity Container

#78 MTDouglas closed 2 months ago
1
Upgrading to RAxML-NG, IQtree, and RAxML-standard

#77 susannah-b closed 10 months ago
0
Upgrade to RAxML-NG

#76 susannah-b closed 11 months ago
0
About Phyloscanner for with-in host

#75 manisenthils closed 1 year ago
4
Couldn't compile software using "make" command

#74 manisenthils closed 1 year ago
1
How to download Phyloscanner!1

#73 manisenthils closed 1 year ago
0
phylotree_analyze defaults to downsampled

#72 evandiego83 closed 9 months ago
4
RAxML failing without error message

#71 ChrisHIV opened 1 year ago
5
Bam files have no reads

#70 Daniele-Pantano closed 2 years ago
3
Installing phyloflows

#69 mmaninetti closed 2 years ago
4
phyloscanner.analyse.trees.R

#68 amcasto closed 9 months ago
1
Error on instaling progject dependencies

#67 LanaZet closed 2 years ago
7
Cannot install Phyloscanner.R.utilities

#66 vtsyvina closed 2 years ago
11
Bam file has more than one references given

#65 simeonhebrew closed 1 year ago
3
ERROR: dependency ‘pegas’ is not available for package ‘phyloscannerR’

#64 ConstantinV closed 3 years ago
1
Issue with CalculateTreeSizeInGenomeWindows.py

#63 BT896 closed 3 years ago
3
Problems running phyloscanner_analyse_trees.R

#62 thednainus closed 3 years ago
4
add functions

#61 XiaoyueXI closed 3 years ago
3
Bootstrapping trees 1st part

#60 evandiego83 opened 3 years ago
3
fail to install phyloscannerR from GitHub

#59 BT896 closed 3 years ago
6
Error with analysing own trees (not made with phyloscanner_make_trees.py)

#58 Steven-Kemp closed 4 years ago
0
Ordev

#57 olli0601 opened 5 years ago
0
Xx zerocounts

#56 olli0601 closed 5 years ago
0
Error installing phyloflows

#55 dianatordoff closed 5 years ago
1
phyloscanner_analyse_trees.R problem

#54 KF-DR closed 9 months ago
6
new network functions

#53 olli0601 closed 5 years ago
0
transmission network code

#52 olli0601 closed 5 years ago
0
Mh devel 2

#51 olli0601 closed 5 years ago
0
PhyloscannerR error: Cannot normalise branch lengths from file without window cooardinates in tree IDs

#50 magosil86 closed 5 years ago
2
PhyloscannerR error: Some trees have duplicate IDs

#49 damientully closed 5 years ago
7
Window coordinates will now be read from tree file names when a direc…

#48 mdhall272 closed 5 years ago
0
Mh devel 2

#47 mdhall272 closed 5 years ago
0
The phyloflow R package provides Bayesian models for source attribution from phyloscanner output, in particular including the case when the study population has not been sampled homogeneously.

#46 olli0601 closed 5 years ago
0
contributing phyloflow R package

#45 olli0601 closed 5 years ago
0
summary_statistics.R Error: All columns in a tibble must be 1d or 2d objects: * Column `tree.id` is NULL

#44 magosil86 closed 5 years ago
18
classify_relationships.R Error in if (is.na(assocs[[node.no]])) { : argument is of length zero

#43 magosil86 closed 5 years ago
4
split_hosts_to_subgraphs.R Error: length(lims) == 2 is not TRUE

#42 damientully closed 5 years ago
5
Seperate analyses or combined dataset

#41 evandiego closed 5 years ago
7
analyse trees.R Error: evaluation nested too deeply: infinite recursion / options(expressions=)?

#40 damientully closed 5 years ago
5
Problem with phyloscanner_analyse_trees.R

#39 SteveKemp closed 5 years ago
12
phyloscannerR no output when only 1 window/tree is used

#38 damientully closed 5 years ago
2
Migrate counting relationship types

#37 olli0601 closed 5 years ago
10
added RCCS example data

#36 olli0601 closed 5 years ago
0
added find.bam.and.references

#35 olli0601 closed 6 years ago
0
add define.stage1.analyses

#34 olli0601 closed 5 years ago
7
TranslateCoords Error

#33 averagehat closed 6 years ago
2
Deal with trees with no branch lengths

#32 mdhall272 opened 6 years ago
0
Error with drawing simplified summary diagram

#31 damientully closed 6 years ago
4