Question: Well-resolved Phylogenetic Dataset
1
gravatar for jnf3769
4.7 years ago by
jnf376940
United States
jnf376940 wrote:

Hello all,

I am looking to test an alignment-free phylogenetic tree building algorithm I wrote. It can perform both gene and species trees. I have already tested it on a single gene primate tree, but I need some more data to further characterize the algorithm. I know there is a lot of data on TreeBASE, but I am having a hard time pulling data down. Additionally, I am generally unaware of which trees are considered well-resolved.

Any info would help greatly

ADD COMMENTlink modified 4.7 years ago by kloetzl1.1k • written 4.7 years ago by jnf376940
2
gravatar for kloetzl
4.7 years ago by
kloetzl1.1k
European Union
kloetzl1.1k wrote:

You might want to use data sets already used in other papers on alignment-free comparisons. Here you can download the data from andi (shameless self-plug). I also have the roseobacter data set from the spaced words paper. Send me a mail, if you are interested.

ADD COMMENTlink written 4.7 years ago by kloetzl1.1k

I have a followup question about the 109 E. coli ST131 strains. In the assemblies (ordered or not), there are multiple nodes per fasta file. Am I right in assuming that that means there are more than one contig per file (that is, the genome was not closed)?

ADD REPLYlink written 4.7 years ago by jnf376940

Yes, those are contigs. A lot of genome projects stay in this state.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by kloetzl1.1k
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