Custom network induces an additional leaf #43
Comments
|
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
<#43>, or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AA4FP7M26IOUFQCI6XQKS7DUJ7SDTANCNFSM5HGPF2SA>
.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
treesdirectory 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:
generates this output:
Thus, the following networks induce hybrid-Lambda to "detach" the hybrid edge and become a leaf:
From there I see that on your networks from the
treesdirectory these leaves only appear when therroot string is missing. However, on my custom networks these are present with or without therstring.Any suggestion would be really appreciated to build my own custom networks as input for hybrid-Lambda.
Best wishes,
Gustavo
The text was updated successfully, but these errors were encountered: