search

hybridLambda / hybrid-Lambda

Hybrid-Lambda is a software package that can simulate gene trees within a rooted species network or a rooted species tree under the Kingman's coalescent or Lambda coalescent process.
http://hybridlambda.github.io/
GNU General Public License v3.0
6 stars 4 forks source link

Custom network induces an additional leaf #43

Open gaballench opened 2 years ago

gaballench commented 2 years ago

Hello Joe,

I have noted that when using a custom network hybrid-Lambda generates gene trees where the hybrid edge "detaches" and becomes a leaf, that is, for the network including the hybrid edge h1#.5:4.0, the leaf h1#.5_1 is present in the gene trees. This behaviour is not recovered in some of the networks available in the trees directory that comes with the program. I tested both versions 0.6.2 and 0.6.3 and the behaviour is independent of the version. v0.6.2 was slightly modified for returning the magnitude of the diff between branches when testing the ultrametricity (see here).

The script: 

#!/usr/bin/bash

# # custom network, not triggering ultrametricity warning, with or without root string
#  "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);"
#  "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;"
# # custom network, triggering ultrametricity warning, with or without root string
#  "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);"
#  "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;"
# # 3_tax_multi_tax_test_hybrid1, with or without root string
#  "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;"
#  "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);"
# # 6_tax_multi_tax_test_hybrid1_topo1, with or without root string
#  "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;"
#  "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);"

VARS=("(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);" "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;" "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);" "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;" "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;" "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);" "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;" "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);")

for i in ${VARS[@]}; do
    echo $i
done

for i in ${VARS[@]}; do
    printf "\nProcessing $i...\n"
    hybrid-Lambdav0.6.2-pathdiff -spcu $i -num 3 -seed 2 -o out0.6.2
    grep "#" out0.6.2_coal_unit
#    cat out0.6.2_coal_unit
    hybrid-Lambdav0.6.3 -spcu $i -num 3 -seed 2 -o out0.6.3
    grep "#" out0.6.3_coal_unit
#    cat out0.6.3_coal_unit
done

rm out0*

generates this output:

(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);
(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;
(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);
(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;
(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;
(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);
((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;
((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);

Processing (((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.2_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.3_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);

Processing (((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.2_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.3_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);

Processing (((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Square diff in paths: 4
Absolute diff in paths: 2
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.2_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.3_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);

Processing (((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Square diff in paths: 4
Absolute diff in paths: 2
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.2_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.3_coal_unit
((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);
((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);
(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);

Processing (((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.2_coal_unit
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Random seed: 2
Produced gene tree files: 
out0.6.3_coal_unit

Processing (((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Square diff in paths: 0.36
Absolute diff in paths: 0.6
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.2_coal_unit
((h1#.5_1:1.717184,C_1:2.317184):1.157862,(A_1:2.232417,B_1:2.232417):1.242629);
(C_1:4.405919,(h1#.5_1:3.321777,(B_1:1.342461,A_1:1.342461):2.579316):0.484142);
(C_1:2.203538,((A_1:1.774547,B_1:1.774547):0.235875,h1#.5_1:1.410423):0.193115);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.3_coal_unit
((h1#.5_1:1.717184,C_1:2.317184):1.157862,(A_1:2.232417,B_1:2.232417):1.242629);
(C_1:4.405919,(h1#.5_1:3.321777,(B_1:1.342461,A_1:1.342461):2.579316):0.484142);
(C_1:2.203538,((A_1:1.774547,B_1:1.774547):0.235875,h1#.5_1:1.410423):0.193115);

Processing ((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Square diff in paths: 0.04
Absolute diff in paths: 0.2
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.2_coal_unit
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.3_coal_unit

Processing ((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);...
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
Square diff in paths: 0.04
Absolute diff in paths: 0.2
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.2_coal_unit
((h1#.5_1:2.260888,(F_1:3.542078,(E_1:1.883584,(B_1:1.048594,D_1:1.248594):0.034991):1.658494):1.118810):0.785922,(A_1:3.022269,C_1:3.022269):0.624541);
(((h1#.5_1:1.056655,C_1:1.656655):0.655545,(((E_1:0.996610,F_1:0.996610):0.646552,D_1:1.043162):0.628633,B_1:1.471795):1.840405):1.390280,A_1:3.702480);
((A_1:1.862379,(C_1:1.385222,h1#.5_1:0.785222):0.477157):1.079919,(B_1:1.495700,((E_1:1.098141,F_1:1.098141):0.265469,D_1:0.763609):0.932091):2.446598);
Default Kingman coalescent on all branches.
Default population size of 10000 on all branches. 
WARNING! NOT ULTRAMETRIC!!!
Random seed: 2
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
WARNING: Gene tree is not ultrametric
Produced gene tree files: 
out0.6.3_coal_unit
((h1#.5_1:2.260888,(F_1:3.542078,(E_1:1.883584,(B_1:1.048594,D_1:1.248594):0.034991):1.658494):1.118810):0.785922,(A_1:3.022269,C_1:3.022269):0.624541);
(((h1#.5_1:1.056655,C_1:1.656655):0.655545,(((E_1:0.996610,F_1:0.996610):0.646552,D_1:1.043162):0.628633,B_1:1.471795):1.840405):1.390280,A_1:3.702480);
((A_1:1.862379,(C_1:1.385222,h1#.5_1:0.785222):0.477157):1.079919,(B_1:1.495700,((E_1:1.098141,F_1:1.098141):0.265469,D_1:0.763609):0.932091):2.446598);

Thus, the following networks induce hybrid-Lambda to "detach" the hybrid edge and become a leaf:

(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);
(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;
(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);
(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;
(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);
((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);

From there I see that on your networks from the trees directory these leaves only appear when the r root string is missing. However, on my custom networks these are present with or without the r string.

Any suggestion would be really appreciated to build my own custom networks as input for hybrid-Lambda.

Best wishes,

Gustavo

shajoezhu commented 2 years ago

Hi Gustavo

When constructing a network, make sure all nodes are labelled, i.e. please label the root as well. In your case, the r node

Best Joe

On Tue, 2 Nov 2021, 13:33 Gustavo A. Ballen, @.***> wrote:

Hello Joe,

I have noted that when using a custom network hybrid-Lambda generates gene trees where the hybrid edge "detaches" and becomes a leaf, that is, for the network including the hybrid edge h1#.5:4.0, the leaf h1#.5_1 is present in the gene trees. This behaviour is not recovered in some of the networks available in the trees directory that comes with the program. I tested both versions 0.6.2 and 0.6.3 and the behaviour is independent of the version. v0.6.2 was slightly modified for returning the magnitude of the diff between branches when testing the ultrametricity (see here https://github.com/gaballench/hybrid-Lambda/tree/verbose-pathdiff).

The script:

!/usr/bin/bash

custom network, not triggering ultrametricity warning, with or without root string# "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);"# "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;"# # custom network, triggering ultrametricity warning, with or without root string# "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);"# "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;"# # 3_tax_multi_tax_test_hybrid1, with or without root string# "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;"# "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);"# # 6_tax_multi_tax_test_hybrid1_topo1, with or without root string# "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;"# "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);"

VARS=("(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);" "(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;" "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);" "(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;" "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;" "(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);" "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;" "((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);") for i in ${VARS[@]}; do echo $idone for i in ${VARS[@]}; do printf "\nProcessing $i...\n" hybrid-Lambdav0.6.2-pathdiff -spcu $i -num 3 -seed 2 -o out0.6.2 grep "#" out0.6.2_coal_unit# cat out0.6.2_coal_unit hybrid-Lambdav0.6.3 -spcu $i -num 3 -seed 2 -o out0.6.3 grep "#" out0.6.3_coal_unit# cat out0.6.3_coal_unitdone

rm out0*

generates this output:

(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);Processing (((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.2_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.3_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Processing (((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.2_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.3_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:5.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:7.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:8.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Processing (((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Square diff in paths: 4Absolute diff in paths: 2WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.2_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.3_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Processing (((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Square diff in paths: 4Absolute diff in paths: 2WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.2_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.3_coal_unit((((A_1:2.291561,B_1:2.291561):2.813411,C_1:5.104972):2.956590,(D_1:5.898695,h1#0.5_1:3.898695):2.162867):1.080899,E_1:9.142461);((D_1:7.822784,(((A_1:2.834647,B_1:2.834647):2.224355,C_1:5.059002):2.132514,h1#0.5_1:5.191516):0.631268):1.370331,E_1:9.193115);(E_1:10.983763,((h1#0.5_1:6.657187,(C_1:6.141945,(A_1:2.412703,B_1:2.412703):3.729242):2.515241):0.759950,D_1:9.417136):1.566627);Processing (((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.2_coal_unitDefault Kingman coalescent on all branches.Default population size of 10000 on all branches. Random seed: 2Produced gene tree files: out0.6.3_coal_unitProcessing (((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Square diff in paths: 0.36Absolute diff in paths: 0.6WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.2_coal_unit((h1#.5_1:1.717184,C_1:2.317184):1.157862,(A_1:2.232417,B_1:2.232417):1.242629);(C_1:4.405919,(h1#.5_1:3.321777,(B_1:1.342461,A_1:1.342461):2.579316):0.484142);(C_1:2.203538,((A_1:1.774547,B_1:1.774547):0.235875,h1#.5_1:1.410423):0.193115);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.3_coal_unit((h1#.5_1:1.717184,C_1:2.317184):1.157862,(A_1:2.232417,B_1:2.232417):1.242629);(C_1:4.405919,(h1#.5_1:3.321777,(B_1:1.342461,A_1:1.342461):2.579316):0.484142);(C_1:2.203538,((A_1:1.774547,B_1:1.774547):0.235875,h1#.5_1:1.410423):0.193115);Processing ((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6)r;...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Square diff in paths: 0.04Absolute diff in paths: 0.2WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.2_coal_unitDefault Kingman coalescent on all branches.Default population size of 10000 on all branches. WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.3_coal_unitProcessing ((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);...Default Kingman coalescent on all branches.Default population size of 10000 on all branches. Square diff in paths: 0.04Absolute diff in paths: 0.2WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.2_coal_unit((h1#.5_1:2.260888,(F_1:3.542078,(E_1:1.883584,(B_1:1.048594,D_1:1.248594):0.034991):1.658494):1.118810):0.785922,(A_1:3.022269,C_1:3.022269):0.624541);(((h1#.5_1:1.056655,C_1:1.656655):0.655545,(((E_1:0.996610,F_1:0.996610):0.646552,D_1:1.043162):0.628633,B_1:1.471795):1.840405):1.390280,A_1:3.702480);((A_1:1.862379,(C_1:1.385222,h1#.5_1:0.785222):0.477157):1.079919,(B_1:1.495700,((E_1:1.098141,F_1:1.098141):0.265469,D_1:0.763609):0.932091):2.446598);Default Kingman coalescent on all branches.Default population size of 10000 on all branches. WARNING! NOT ULTRAMETRIC!!!Random seed: 2WARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricWARNING: Gene tree is not ultrametricProduced gene tree files: out0.6.3_coal_unit((h1#.5_1:2.260888,(F_1:3.542078,(E_1:1.883584,(B_1:1.048594,D_1:1.248594):0.034991):1.658494):1.118810):0.785922,(A_1:3.022269,C_1:3.022269):0.624541);(((h1#.5_1:1.056655,C_1:1.656655):0.655545,(((E_1:0.996610,F_1:0.996610):0.646552,D_1:1.043162):0.628633,B_1:1.471795):1.840405):1.390280,A_1:3.702480);((A_1:1.862379,(C_1:1.385222,h1#.5_1:0.785222):0.477157):1.079919,(B_1:1.495700,((E_1:1.098141,F_1:1.098141):0.265469,D_1:0.763609):0.932091):2.446598);

Thus, the following networks induce hybrid-Lambda to "detach" the hybrid edge and become a leaf:

(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);(((h1#0.5:4.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0);(((h1#0.5:2.0,D:4.0):3.0,((A:2.0,B:2.0):3.0,(C:2.0)h1#0.5:3.0):2.0):2.0,E:9.0)r;(((B:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);((((B:1,(D:0.6,(E:0.6,F:0.6)s5:0.6)s4:0.6)s3:.6)h1#.5:.6,A:1.2)s1:.6,(h1#.5:.6,C:1.2)s2:.6);

From there I see that on your networks from the trees directory these leaves only appear when the r root string is missing. However, on my custom networks these are present with or without the r string.

Any suggestion would be really appreciated to build my own custom networks as input for hybrid-Lambda.

Best wishes,

Gustavo

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/hybridLambda/hybrid-Lambda/issues/43, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA4FP7M26IOUFQCI6XQKS7DUJ7SDTANCNFSM5HGPF2SA .