iqtree output as newick or nexus format

Question

[hafiz.talhamalik]

I am using treetime and I need nexus / newick format as an input. my question is how can I generate this file for input in treetime ?? or anyother tool to serve this purpose ?? I used iqtree but the output file is not in these formats

Answer 1

[Dave Carlson]

The .treefile output file produced by IQ-TREE is in Newick format. Are you sure that's the file you're using as input for treetime? If so, what's the error you're receiving?

[hafiz.talhamalik]

oh thanx for the help, I was using .iqtree file as an input.. this one helped but now there error is in alignment file.

Traceback (most recent call last):
File "/mnt/d/anaconda3/bin/treetime", line 12, in <module>
return_code = params.func(params)

File "/mnt/d/anaconda3/lib/python3.9/site-packages/treetime/wrappers.py", line 1004, in estimate_clock_model raise e File "/mnt/d/anaconda3/lib/python3.9/site-packages/treetime/wrappers.py", line 999, in estimate_clock_model myTree = TreeTime(dates=dates, tree=params.tree, aln=aln, gtr='JC69', File "/mnt/d/anaconda3/lib/python3.9/site-packages/treetime/sequence_data.py", line 186, in aln raise MissingDataError("SequenceData: loading alignment failed... " + str(in_aln)) treetime.MissingDataError: SequenceData: loading alignment failed... all.fasta

[Dave Carlson]

I've never actually used TreeTime and I don't know exactly what the issue is, but it looks like perhaps there is some sort of mismatch between the sequences in your alignment and the terminal branches in your tree. Or perhaps a formatting issue with your alignment.

I would double check to confirm that the sequence names in your alignment file exactly match the sequence names in your tree and the that the alignment is in fasta format.

[hafiz.talhamalik]

Error was due to a problem in the alignment fasta file. mafft was causing some issue which lead to corrupt fasta file.