Dear all, Please, if I have multiple sequence alignments for parts of a virus genome; how can I end up with phylogenetic tree (circular tree) showing bootstrap & p distance on it? Also how can I plot the p distance distribution? Many Thanks in advance
There is a lot of information on the World Wide Web about building phylogenetic trees, but it's all quite sparse, meaning that you'll have to piece it all together to get what you want.
This first tutorial may be of use to you in order to help you to get from your FASTA sequences to a clustering object / tree structure: Using R to Caculate Genetic Distance and Generate Phylogenetic tree. It utilises the ape package in R. NB - the typeo in the title is not my own.
Hopefully this helps you somewhat.
- 1) p_dis_X.mat is p distance matrix X=(1,2....100); To using the the part of the sites and new the nj-tree as above. Repeat For the NN times. X=(1,2....100);
PHYLIPNEW-3.69.650/bin/fneighbor -datafile p_dis_X.matrix -outfile tree.out1_X.txt -matrixtype s -treetype n -outtreefile tree.out2_X.tre
- 2) merge the all the put back sampling NJ-tree and construct boostrap nj-tree.
cat tree.out2_*.tre > ALLtree_merge.tre PHYLIPNEW-3.69.650/bin/fconsense -intreefile ALLtree_merge.tre -outfile out -treeprint Y
- 3) construct nj-tree and present it (need deal with Other software)
# The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file Final_boostrap.tre]