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PHYLIP package

Last update on the 25th of February, 2018

Here I build trees with neighbor-joining algorithm in PHYLIP package and compare the results with ones obtained from MEGA 7. The used implementation of PHYLIP is embassy-phylip as a part of EMBOSS package.

Table of downloads
File Link
A user's guide guide.pdf

Tree building

First, the distance matrix is calculated with fprotdist program. It takes multiple alignment for input and outputs the matrix. Then, fneighbor infer phylogeny with N-J or UPGMA method. Output files are:

  • pseudo-graphics tree with allowed negative branch lengths (*.fneighbor by default);
  • Newick tree formula (.treefile).

The tree can be visualized from tree formula file with fdrawtree and fdrawgram programs. Former makes unrooted tree, latter — rooted cladogram. Both programs plot .ps file (can be changed to .bmp). The .ps file can be transformed into .png with ps2png program in tth-common package.

Tree comparison

Fig. 1. Comparison of trees build by (A) MEGA and (B) PHYLIP.
Equal non-trivial branches significant for comparison are coloured green, non-equal non-trivial branch is coloured red.

As it is seen from fig. 1, trees are almost identical except for placement of RALSO and NEIMA towards two other subtrees. This can be explained with the fact that the distance between two controversial nodes (1-2 and 2-3) is relatively small, that means sequences of RALSO and NEIMA RL1 protein differ relatively slightly and distant matrices might be ambiguous.

Fig. 2. Distance matrix obtained with PHYLIP.
Tree numbers are equal to those in fig. 1. Distances to NEIMA and RALSO are bolded, the greater values are coloured with red.

The examination of matrix file obtained with fprotdist indeed exposes ambiguity (fig. 2). Leafs from the same subtree relate in different way to NEIMA and RALSO in terms of distance. So, another explanation of non-identity of trees obtained with PHYLIP and MEGA is that N-J method is heurisitc thus different runs may result in slightly different trees.

User's guide to plotting utilities

guide.pdf

Unfortunately, EMBOSS fdrawtree and fdrawgram do not respond to changed flag settings like width of the tree or defining branch lengths. The only working parameters were input, output and previewer. To launch and finish any of two programs with output file, -preview n has to be taped unless one's have any display device like X Windows server.

Thus, PHYLIP's original drawtree and drawgram were under consideration. A user's guide to them can be downloaded from the downloads table above.