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kappa for seq-gen

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commit a89415f48a1fb08c436f116a3b21d233eb5ddb4d 1 parent b97917d
Jeet Sukumaran authored

Showing 1 changed file with 6 additions and 1 deletion. Show diff stats Hide diff stats

  1. +6 1 dendropy/interop/seqgen.py
7 dendropy/interop/seqgen.py
@@ -102,7 +102,7 @@ def __init__(self, strongly_unique_tempfiles=False):
102 102 self.gamma_cats = None
103 103 self.prop_invar = None
104 104 self.state_freqs = None
105   - self.ti_tv = None
  105 + self.ti_tv = 0.5 # = kappa of 1.0, i.e. JC
106 106 self.general_rates = None
107 107 self.ancestral_seq = None
108 108 self.output_text_append = None
@@ -117,6 +117,11 @@ def _set_rng(self, rng):
117 117 self._rng = rng
118 118 rng = property(_get_rng, _set_rng)
119 119
  120 + def _get_kappa(self):
  121 + return float(self.ti_tv) / 2
  122 + def _set_kappa(self, kappa):
  123 + self.ti_tv = kappa * 2
  124 +
120 125 def _compose_arguments(self):
121 126 """
122 127 Composes and returns a list of strings that make up the arguments to a Seq-Gen

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