<commit_before>I found this on https://groups.google.com/forum/#!topic/phyml-forum/yeIwFkwsI8c posted 4/16/2014:
[And then I modified it so that the phyml program exits after printing
the matrix and therefore doesn't even create a tree; makes it faster,
and all we need for hiv-founder-id is the matrix.]

In the function Dist_And_BioNJ (in utilities.c) replace the following block of
instructions:
>>
  Bionj(mat);
  tree      = mat->tree;
  tree->mat = mat;

  return tree;
<<

with
>>
  Bionj(mat);
  tree      = mat->tree;
  tree->mat = mat;
  Print_Mat(mat);
  // Paul added this to skip making the tree, just output the distance
  // matrix and exit.  When compiling with this, phyml should be
  // renamed eg to phyml_matrixonly 
  Warn_And_Exit("");

  return tree;
<<

and recompile. That should do the trick.

Regards,

-<NAME>-<commit_msg>further patching for the impatient<commit_after>I found this on https://groups.google.com/forum/#!topic/phyml-forum/yeIwFkwsI8c posted 4/16/2014:
[And then I modified it so that the phyml program exits after printing
the matrix and therefore doesn't even create a tree; makes it faster,
and all we need for hiv-founder-id is the matrix.]

In the function Dist_And_BioNJ (in utilities.c) replace the following block of
instructions:
>>
  Bionj(mat);
  tree      = mat->tree;
  tree->mat = mat;

  return tree;
<<

with
>>
  Bionj(mat);
  tree      = mat->tree;
  tree->mat = mat;
  Print_Mat(mat);
  // Paul added this to skip making the tree, just output the distance
  // matrix and exit.  When compiling with this, phyml should be
  // renamed eg to phyml_matrixonly 
  Warn_And_Exit("");

  return tree;
<<

and recompile. That should do the trick.

Regards,

-<NAME>-

### Paul adds, to remove the 4000 sequence limit from phyml_matrixonly:
In file utilities.h, raise the limit from 4K to eg 100K:
149c149
< #define  N_MAX_OTU         100000
---
> #define  N_MAX_OTU           4000
{'fraction_non_alphanumeric': 0.09664082687338502, 'fraction_numerical': 0.020671834625323, 'mean_word_length': 3.3800904977375565, 'pattern_counts': {'":': 0, '<': 14, '<?xml version=': 0, '>': 22, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7281344', 'n_tokens_mistral': 693, 'n_tokens_neox': 628, 'n_words': 241}