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I run the PhyRex with the input files in example/phyrex. And the command line is ./phyrex -- xml=../examples/phyrex/flu.exl
The output is something like this
. 83 patterns found (out of a total of 1434 sites).
. 1346 sites without polymorphism (93.86%).
. Starting tree: BioNJ
. Tree topology search: spr
. Processing 1 data set ( ./h1n1.nxs )
| |
| ./h1n1.nxs (partition element 0) |
|_______________________________________________________________________|
. Number of rate classes: 4
. Model of rate variation: Gamma
. Gamma shape parameter value: 1.00
Optimise: yes
. Relative average rate: 1.000000
. Mixture class 1
Relative substitution rate: 0.136954
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 0
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 2
Relative substitution rate: 0.476752
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 1
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 3
Relative substitution rate: 1.000000
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 2
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 4
Relative substitution rate: 2.386294
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 3
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
| |
| Model summary table |
|_______________________________________________________________________|
Partition element 0 0 0 0
State frequencies a a a a
Branch lengths a a a a
Rate matrix a a a a
I run the PhyRex with the input files in example/phyrex. And the command line is
./phyrex -- xml=../examples/phyrex/flu.exl
The output is something like this
. 83 patterns found (out of a total of 1434 sites).
. 1346 sites without polymorphism (93.86%).
. Starting tree: BioNJ
. Tree topology search: spr
. Processing 1 data set ( ./h1n1.nxs )
| |
| ./h1n1.nxs (partition element 0) |
|_______________________________________________________________________|
. Number of rate classes: 4
. Model of rate variation: Gamma
. Gamma shape parameter value: 1.00
Optimise: yes
. Relative average rate: 1.000000
. Mixture class 1
Relative substitution rate: 0.136954
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 0
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 2
Relative substitution rate: 0.476752
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 1
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 3
Relative substitution rate: 1.000000
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 2
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
. Mixture class 4
Relative substitution rate: 2.386294
Rel. rate freq. (> 0 rates): 0.250000
Rate class number: 3
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: no
Rate matrix weight: 1.000000
Optimise nucletide freq.: no
Equ. freq. weight: 1.000000
| |
| Model summary table |
|_______________________________________________________________________|
Partition element 0 0 0 0
State frequencies a a a a
Branch lengths a a a a
Rate matrix a a a a
. Computing pairwise distances...
. Building BioNJ tree...Segmentation fault (core dumped)
I tried to change the initial tree to random but the problem is same.
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