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kappa for seq-gen

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1 parent b97917d commit a89415f48a1fb08c436f116a3b21d233eb5ddb4d @jeetsukumaran committed Apr 9, 2012
Showing with 6 additions and 1 deletion.
  1. +6 −1 dendropy/interop/seqgen.py
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7 dendropy/interop/seqgen.py
@@ -102,7 +102,7 @@ def __init__(self, strongly_unique_tempfiles=False):
self.gamma_cats = None
self.prop_invar = None
self.state_freqs = None
- self.ti_tv = None
+ self.ti_tv = 0.5 # = kappa of 1.0, i.e. JC
self.general_rates = None
self.ancestral_seq = None
self.output_text_append = None
@@ -117,6 +117,11 @@ def _set_rng(self, rng):
self._rng = rng
rng = property(_get_rng, _set_rng)
+ def _get_kappa(self):
+ return float(self.ti_tv) / 2
+ def _set_kappa(self, kappa):
+ self.ti_tv = kappa * 2
+
def _compose_arguments(self):
"""
Composes and returns a list of strings that make up the arguments to a Seq-Gen

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