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This article will explain in detail what is the use of FastTree software for you. The editor thinks it is very practical, so I share it with you for reference. I hope you can get something after reading this article.

FastTree is a software that builds evolutionary tree based on maximum likelihood method. Its most important feature is that it runs fast and supports millions of sequences to build trees. Officially, for large comparison datasets, FastTree is 10 to 1000 times faster than phyml or RAxML. The official website is as follows

Http://www.microbesonline.org/fasttree/

FastTree supports the construction of evolutionary trees of nucleic acids and proteins. For nucleic acids, alternative models include the following

JC

GTR

The default model is JC.

For proteins, alternative models include the following

JTT

LG

WAG

The default model is JTT.

Using different test data sets, the running speeds of different replacement models of fastTree and RAxML and PhyML are compared. The results are as follows

For protein sequences, FastTree runs more than 1000 times faster than the other two softwares, and for tens of thousands of sequences, the other two softwares run too long to tolerate; for nucleic acid sequences, the default JC model is the fastest, the GTR model is slightly slower, and the other two softwares are also slow.

In addition to the fast running speed, the accuracy of FastTree is also satisfactory. the comparison results are as follows.

For tens of thousands of nucleic acid sequences, only FastTree, NJ and Clearcut have results, and the accuracy of FastTree is the highest. From this, it can be seen that FastTree is one of the best choices for the evolutionary tree analysis of tens of thousands of nucleic acid sequences; for protein sequences, the accuracy of FastTree is slightly lower than that of RAxML and PhyML.

Considering the running speed and the accuracy of tree building, FastTree is one of the best evolutionary tree construction software.

We can download executable files directly from the official website.

FastTree requires that the input multiple sequence alignment result is in FASTA or Phylip format. For the construction of protein evolutionary tree, the basic usage is as follows.

FastTree protein.fasta > tree

You can also choose LG or WAG to replace the model, using the following

FastTree-lg protein.fasta > treeFastTree-wag protein.fasta > tree

For nucleic acid sequences, the basic usage is as follows

FastTree-nt nucleotide.fasta > tree

You can also choose GTR to replace the model, using the following

FastTree-nt-gtr nucleotide.fasta > tree

The tree file generated by default is in Newick format and can be imported into software such as figTree or TreeViewer for viewing.

This is the end of this article on "what is the use of FastTree software?". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

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