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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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The tree built from fastANI .matrix data should be called phylogram or cladogram? #73

Closed limin321 closed 4 years ago

limin321 commented 4 years ago

Sorry, my question may be very basic, but it is a question for me.

I created a tree from xx.matrix by running fastANI. The topology almost matches the topology of my phylogenetic tree built from multilocus sequences. However, the .matrix created by fastANI is based on ANI value, but when creating a tree, it is converted to phylip format. can anyone please explain to me it is a phylogram or cladogram??

Your help is greatly appreciated. Best, Limin

cjain7 commented 4 years ago

I don't do phylogenetics research, but my understanding is that you could build either phylogram or cladogram depending upon your choice of tree-making tool (and its parameters). Documentation of the tree-making tool might serve as a better reference. Although by just looking at the tree, you should be able to tell its type (?)

limin321 commented 4 years ago

I don't do phylogenetics research, but my understanding is that you could build either phylogram or cladogram depending upon your choice of tree-making tool (and its parameters). Documentation of the tree-making tool might serve as a better reference. Although by just looking at the tree, you should be able to tell its type (?)

No, the tree created doesn't have branch length. Because I first converted the fastANI pairwise distance to fastANI.phylip; then created the tree using 

Rscript bionj_tree.R output.phylip ./output.newick

That is why I am not sure it should be phylogram or cladogram.

If use normal tools, like iqTree, I could tell it is phylogram.

Any more thoughts?

Best, Limin

cjain7 commented 4 years ago

If the tree doesn't have branch length, then isn't it cladogram (?) Unfortunately I lack bandwidth to dig deeper.

limin321 commented 4 years ago

If the tree doesn't have branch length, then isn't it cladogram (?) Unfortunately I lack bandwidth to dig deeper.

Thank you so much. If I get answer one day, I will come back and leave a message here.