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VCF2Dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix and tree based Variant Call Format


if you can't get the p_dis.nwk tree file but had the p-distance matrix [p_dis.mat], here are the 3 Other ways to get the tree file.

Method 1 : online WebSite

Choose one of A/B
A. Upload the web fneighbor(http://emboss.toulouse.inra.fr/cgi-bin/emboss/fneighbor?_pref_hide_optional=1) ，the Click the Run fneighbor bottom . then you can get the output file datafile.treefile
B. Upload the p_dis.mat to the website fastme (http://www.atgc-montpellier.fr/fastme/), select Data Type to the Distance matrix ,Click the bottom twist execute & email results. you will get the p_dis_mat_fastme-tree.nwk , and Email not mandatory;

Run MEGA # The MEGA (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file [p_dis_mat_fastme-tree.nwk]

Method 2 : PHYLIPNEW

Use the PHYLIPNEW to construct nj-tree
How to Install PHYLIPNEW please Click on here or Click on here(Chinese)

      #    3.1 Run  PHYLIP
      #   After p_distance done , software PHYLIPNEW 3.69 (http://evolution.genetics.washington.edu/phylip.html) ,with neighbor-joining method can was used to construct the phylogenetic tree on the basis of this  p_distance matrix;
       
           PHYLIPNEW-3.69.650/bin/fneighbor  -datafile p_dis.matrix  -outfile tree.out1.txt -matrixtype s -treetype n -outtreefile tree.out2.tre

      #    3.2 Run  MEGA
      #    The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file [tree.out2.tre]

Method 3 : R script with ape

      #    3.1 Run  R Rscript
		Rscript  exemple1/vistreecode.r    p_dis.mat
      #    3.2 Run  MEGA
      #    The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file [tree.out2.tre]
    1. you can see the neighbor-joining tree and save it as PDF format

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