xavierdidelot ClonalFrameML issues

xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

GNU General Public License v3.0

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Correlate positions between input alignment/graphical output

#155 juliaped closed 2 months ago
1
N/A on posterior means on the per branch model

#154 PaulineGachanja closed 2 months ago
2
Segmentation fault after reading tree

#153 xonq closed 2 months ago
2
option -fasta_file_list true?

#152 goshng closed 4 months ago
1
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label was not expected

#151 maxibor closed 7 months ago
2
What do you mean I don't understand the output file

#150 17863952296 closed 10 months ago
1
nonrecombinant alignment output empty

#149 lagphase closed 11 months ago
1
Fix std::binary_function depreciation error

#148 moorembioinfo closed 11 months ago
0
how to create the msa file for fragmented genomes

#147 jianshu93 closed 1 year ago
1
Some genomes not displaying on tree

#146 tbazilegith closed 1 year ago
6
Script cfml_results.R not found

#145 tbazilegith closed 1 year ago
4
Fix R/theta, 1/delta and Nu

#144 fernanda-ordonez closed 1 year ago
0
contructed a new whole genome alignment

#143 liuxiong714 closed 1 year ago
1
Can I use SNP multiple sequence alignment matrix and a tree build based on it as inputs?

#142 CJJ8848 closed 1 year ago
5
R script plot colours are not explained

#141 sam-spence closed 1 year ago
3
Inquiry on difference of Recombination Visualization between cfml_results.R and Phandango

#140 Tonny-zhou closed 1 year ago
1
High recombination sequence detection

#139 conmeehan closed 1 year ago
3
ERROR: Token: ((( Found left bracket but no right bracket

#138 ne1al closed 1 year ago
1
Are there any detailed description of the output pdf from cfml_results.R?

#137 1996xjm closed 1 year ago
1
std::bad_alloc problem

#136 DorothyTamYiLing closed 1 year ago
1
Is it better to order genes by the reference genome for a xmfa file ???

#135 yayahoho1 closed 1 year ago
2
why the r/m I calculated is so small using a subclone of subclone of klebsiella pneumoniae

#134 xuechunxu closed 2 years ago
1
Recombination filtered output vs importation_status.txt

#133 raufs closed 2 years ago
1
R values for calculation of R*delta

#132 cbreusing closed 2 years ago
2
how to calculate the r/m value for subclade of a tree？

#131 Tonny-zhou closed 2 years ago
4
segmentation fault (core dumped)

#130 annarerra closed 2 years ago
1
input alignment for ClonalFrameML

#129 annarerra closed 2 years ago
1
How to solve problems about "makefile", Thanks a lot!

#128 nolan12333 closed 2 years ago
2
ClonalFrameML for analyses of gene families

#127 juliaped closed 2 years ago
2
node labels

#126 annarerra closed 2 years ago
2
ERROR: incompatible with a bifurcating unrooted tree

#125 LeonardosMageiros closed 3 years ago
1
convert_NewickTree_to_marginal_tree()

#124 ga23981 closed 3 years ago
2
Recombination events total

#123 martinastoycheva closed 3 years ago
1
Question: xmfa format?

#122 nbawe closed 3 years ago
7
xmfa format question; error: Segmentation fault (core dumped)

#121 agor0 closed 3 years ago
1
cfml_results.R error

#120 maguileraf closed 3 years ago
8
Question: r/m calculation with CI95%!

#119 maesaar closed 3 years ago
4
Question: Concatenated sequences as input?

#118 nbawe closed 3 years ago
7
Using Mummer output as CFML input

#117 edsonmachado closed 3 years ago
1
Segmentation fault

#116 spencer411 closed 3 years ago
2
Can I get branch-specific values for R/Theta, 1/delta and nu from a standard CFML run?

#115 jodsikorski closed 3 years ago
2
95% CI for r/m

#114 jodsikorski closed 3 years ago
7
R script location

#113 martinastoycheva closed 3 years ago
1
added ppc64le arch on yaml file.

#112 srinivas32 closed 3 years ago
0
Interpreting a long blue line in output figure

#111 megaptera-helvetiae closed 4 years ago
1
FASTA_to_nucleotide(): unsupported base error when using .xmfa file

#110 Jwebster89 closed 4 years ago
3
different outputs with different parameters, how to choose the rihgt one?

#109 cheerupgirls closed 4 years ago
1
Calculate nucleotide diversity within and outside the clonal frame

#108 megaptera-helvetiae closed 4 years ago
1
Drake's rule and molecular evolution

#107 megaptera-helvetiae closed 4 years ago
1
ClonalFrameML not producing all outputs.

#106 izakbed closed 4 years ago
4