Troubleshooting PHYLIP: Common Errors and Fixes

3) Common workflow examples

A — Distance-based tree from DNA (Neighbor-Joining)

1. Run dnadist to compute distance matrix:
   • Command: dnadist
   • Input: choose model (e.g., Jukes-Cantor or Kimura 2-parameter), provide “infile”.
   • Output: “outfile” (distances) and “outtree” (if program generates).
2. Run neighbor to build tree:
   • Command: neighbor
   • Input: it reads the distance matrix (default “infile” or “outfile” from dnadist).
   • Output: “outtree” (Newick) and “outfile” (details).

B — Parsimony from DNA

1. Run pars (or dnapars):
   • Command: dnapars
   • Input: “infile” with aligned DNA sequences.
   • Options: search strategy, randomization, outgroup.
   • Output: “outtree”, “outfile”, and “trees” (if multiple).

C — Protein analysis (distance or parsimony)

• For distances: protdist (choose substitution matrix like JTT), then neighbor.
• For parsimony: protpars.

D — Maximum likelihood (protein or DNA)

• Use proml for protein ML; dnaml for DNA ML.
• Choose model parameters (rate variation, transition/transversion ratio, empirical frequencies).
• Outputs: likelihood scores, tree file.

E — Bootstrapping to assess support

1. Generate bootstrap replicates with seqboot:
   • Command: seqboot
   • Input: “infile”, choose number of replicates (e.g., 1000).
   • Output: “outfile” containing replicates.
2. For each replicate, run analysis (e.g., dnadist + neighbor). PHYLIP can pipeline: run dnadist on seqboot output, then neighbor.
3. Use consense to build consensus tree with bootstrap proportions from tree files.

4) Running non-interactively

• Many PHYLIP programs have interactive prompts; you can automate by providing a control file or using here-documents. Example (bash):

  Code
  Copy CodeCopied
  printf “Y J
  
   
  ” | dnadist < infile > dnadist.out 

  or create a parameter file and redirect stdin.

5) Interpreting outputs

• outtree/newick: tree topology in Newick format for viewing with tree viewers (FigTree, iTOL).
• outfile: program-specific report (distances, scores, steps).
• bootstrapped consensus: support values on internal nodes.

6) Practical tips

• Align sequences first (MAFFT, MUSCLE) before PHYLIP.
• For proteins, choose appropriate substitution matrix and consider gamma-distributed rates.
• Check sequence names: PHYLIP’s strict name length (older versions limited to 10 characters); use newer PHYLIP or adjust names.
• Use small test dataset to verify command options before large runs.
• For large datasets or ML analyses, consider modern tools (RAxML, IQ-TREE) for speed and model features.

7) Minimal example: DNA NJ with bootstrapping (commands)

1. Align sequences to produce “infile” (PHYLIP format).
2. Bootstrap:
   • seqboot (choose 100 replicates)
   • dnadist on seqboot output
   • neighbor on dnadist output
   • consense on resulting trees
3. View “consensus” tree in a viewer.

If you want, I can generate exact example command sequences and sample input files for your dataset (assume DNA or protein and number of sequences).