Comments (4)
xavierdidelot
commented on August 20, 2024
Hi Michelle,
Could you try with just the first two genes to see if that works (ie truncating your xmfa file after the second '=' symbol). If not, could you send me this file plus your tree so I can see what's wrong?
Best wishes,
Xavier
from clonalframeml.
mhulin
commented on August 20, 2024
Hi Xavier,
It is working for 2 genes!
Best wishes
Michelle
from clonalframeml.
xavierdidelot
commented on August 20, 2024
Ok, then keep adding genes until it stops working, and try and see what's wrong with the problematic gene (-:
from clonalframeml.
mhulin
commented on August 20, 2024
Hi Xavier,
I realised the issue was with the xmfa - I had just concatenated fasta files rather than alignments! Thank you for your help, it is working now
Many thanks
Michelle
from clonalframeml.
Related Issues (20)
- Is it better to order genes by the reference genome for a xmfa file ??? HOT 2
- std::bad_alloc problem HOT 1
- Are there any detailed description of the output pdf from cfml_results.R? HOT 1
- ERROR: Token: ((( Found left bracket but no right bracket HOT 1
- High recombination sequence detection HOT 3
- Inquiry on difference of Recombination Visualization between cfml_results.R and Phandango HOT 1
- R script plot colours are not explained HOT 3
- Can I use SNP multiple sequence alignment matrix and a tree build based on it as inputs? HOT 5
- contructed a new whole genome alignment HOT 1
- Fix R/theta, 1/delta and Nu
- Script cfml_results.R not found HOT 4
- Some genomes not displaying on tree HOT 6
- how to create the msa file for fragmented genomes HOT 1
- nonrecombinant alignment output empty HOT 1
- What do you mean I don't understand the output file HOT 1
- ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label was not expected HOT 2
- option -fasta_file_list true? HOT 1
- Segmentation fault after reading tree HOT 2
- N/A on posterior means on the per branch model HOT 2
- Correlate positions between input alignment/graphical output HOT 1
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