Searched refs:exclude_sites (Results 1 – 5 of 5) sorted by relevance
| /dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
| H A D | alignment.h | 308 int exclude_sites, const char *ref_seq_name);
311 int exclude_sites = 0, const char *ref_seq_name = NULL);
314 int exclude_sites = 0, const char *ref_seq_name = NULL);
317 int exclude_sites = 0, const char *ref_seq_name = NULL, bool print_taxid = false);
320 int exclude_sites = 0, const char *ref_seq_name = NULL);
323 … int exclude_sites = 0, const char *ref_seq_name = NULL, bool print_taxid = false);
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| H A D | superalignment.h | 239 const char *aln_site_list = NULL, int exclude_sites = 0,
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| H A D | alignment.cpp | 2575 int exclude_sites, const char *ref_seq_name) in buildRetainingSites() argument
2618 if (exclude_sites & EXCLUDE_GAP) { in buildRetainingSites()
2624 if (exclude_sites & EXCLUDE_INVAR) { in buildRetainingSites()
2631 if (exclude_sites & EXCLUDE_UNINF) { in buildRetainingSites()
2671 int exclude_sites, const char *ref_seq_name) in printFasta() argument
2674 buildRetainingSites(aln_site_list, kept_sites, exclude_sites, ref_seq_name); in printFasta()
2735 int exclude_sites, const char *ref_seq_name) { in printAlignment() argument
2756 int exclude_sites, const char *ref_seq_name) { in printAlignment() argument
2759 printPhylip(out, append, aln_site_list, exclude_sites, ref_seq_name); in printAlignment()
2762 printFasta(out, append, aln_site_list, exclude_sites, ref_seq_name); in printAlignment()
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| H A D | superalignment.cpp | 1426 const char *aln_site_list, int exclude_sites, in printAlignment() argument
1430 concat->printAlignment(format, out, append, aln_site_list, exclude_sites, ref_seq_name); in printAlignment()
1446 int exclude_sites = (params.aln_nogaps) ? EXCLUDE_GAP : 0; in printSubAlignments() local
1447 …pit)->printAlignment(params.aln_output_format, filename.c_str(), false, NULL, exclude_sites, NULL); in printSubAlignments()
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| /dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
| H A D | phyloanalysis.cpp | 3332 int exclude_sites = 0; in convertAlignment() local
3334 exclude_sites += EXCLUDE_GAP; in convertAlignment()
3336 exclude_sites += EXCLUDE_INVAR; in convertAlignment()
3340 exclude_sites, params.ref_seq_name); in convertAlignment()
3354 exclude_sites, params.ref_seq_name); in convertAlignment()
3360 exclude_sites, params.ref_seq_name); in convertAlignment()
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