RE: dating tree - Githubissues

Hello,

You're providing the following dating tree:

17 1
((((Potamogeton_acutifolius,(Spirodela_intermedia,Amorphophallus_konjac)),(Acanthochlamys_bracteata,(Dioscorea_alata,Dioscorea_rotundata))'>0.5600<1.2863')'>0.8360<1.2863',(Acorus_americanus,Acorus_tatarinowii))'>0.8360<1.2863',((((Tetracentron_sinense,Trochodendron_aralioides),(Buxus_austroyunnanensis,Buxus_sinica))'>1.1080<1.2863',(Nelumbo_nucifera,(Telopea_speciosissima,Protea_cynaroides)))'>1.1080<1.2863',(Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2))'>1.1080<1.2863')'>1.2720<2.4720';

I understand that I need to replace the "Aquilegia_coreulea" branches with my species. but what about the branch lengths? Do i need to generate a new species tree including all those species plus my species?

What if I used the same species that I used in the orthology analysis?

thanks

Hi, the starting tree requires only topology and fossil calibrations but no branch length. The species you put in the tree is dependent upon the phylogenetic location of your WGD such that other species in the tree should not share the WGD to be dated except for your focal species.

Thank you for the quick reply. I need a bit more clarification on how to modify this tree for my species. A couple more questions:

Are the ap1 and ap2 the upper and lower CI of the peak from the Anchor Ks distribution of Aquilegia_coerulea.tsv.ks.tsv? If not what are they?

`` 17 1 ((((Potamogeton_acutifolius,(Spirodela_intermedia,Amorphophallus_konjac)),(Acanthochlamys_bracteata,(Dioscorea_alata,Dioscorea_rotundata))'>0.5600<1.2863')'>0.8360<1.2863',(Acorus_americanus,Acorus_tatarinowii))'>0.8360<1.2863',((((Tetracentron_sinense,Trochodendron_aralioides),(Buxus_austroyunnanensis,Buxus_sinica))'>1.1080<1.2863',(Nelumbo_nucifera,(Telopea_speciosissima,Protea_cynaroides)))'>1.1080<1.2863',(my_species_ap1,my_species_ap2))'>1.1080<1.2863')'>1.2720<2.4720';


In the above example, I added my species. Are the numbers that come after it the peak mode, lower and upper CI? if not what are they, and how I can get them for my species. 

Thank you,

Let's make it clear step by step. First, have you ever used mcmctree? Could you please show me the starting tree you used in your last usage of mcmctree.

So far in the analysis, I only used a specie tree (4species.nwk) to do the corrected ks distribution of my species (spu.cds). the species tree is below. it includes divergence times.

((Sly.cds:113.97482000,(Spu.cds:97.85759000,Dlo.cds:97.85759000)'14':16.11723000)'13':11.14478000,Cfo.cds:125.11960000);

Here is the commands :

wgd dmd --globalmrbh Spu.cds Dlo.cds Sly.cds Cfo.cds -oi -f Spu.cds -o wgd_globalmrbh -n 12

wgd ksd wgd_globalmrbh/global_MRBH.tsv Spu.cds Dlo.cds Sly.cds Cfo.cds -o wgd_globalmrbh_ks -n 36

wgd viz -d wgd_globalmrbh_ks/global_MRBH.tsv.ks.tsv -fa Spu.cds \
-epk ../whole-panarome/wgd_ksd/Spu.cds.tsv.ks.tsv \
-ap ../whole-panarome/wgd_syn/iadhore-out/anchorpoints.txt \
-sp 4speices.nwk -o wgd_viz_mixed_Ks --plotelmm --plotapgmm --reweight --plotkde --classic

Note that for rate correction the species tree requires only the topology. Did you use mcmctree to calculate the divergence time?

I understood that about the rate correction. but does including divergence time cause any harms, or misinterpretation by the algorithm? Do I need to redo the correction with topology-only species tree?

No, I didn't use mcmctree to calculate divergence time. I obtained it directly from "http://www.timetree.org/". then i compered the divergence times to what is known in the literature. it seemed accurate to me,

The extra divergence time in the species tree would be simply ignored in the rate correction analysis. Thus, you don't need to redo this part of analysis. I really suggest first having a glance of the tutorial for mcmctree before you go any deeper into molecular dating, which will help you understand better the species tree issue that's unclear to you.

Hey: would you mind keeping this open for a bit longer. I haven’t completed this part yet. I just ran into computer problems and trying to fix them first. Still haven’t figured the tree part.

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From: heche-psb @.> Sent: Wednesday, June 12, 2024 1:58:49 AM To: heche-psb/wgd @.> Cc: Magdy S Alabady @.>; Author @.> Subject: Re: [heche-psb/wgd] RE: dating tree (Issue #36)

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Closed #36https://github.com/heche-psb/wgd/issues/36 as completed.

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Hi I am getting the following error in the dating step.

$ wgd focus --protcocdating --aamodel lg wgd_dmd_ortho/merge_focus_ap.tsv -sp dating_tree.nw -o wgd_dating \
> -d mcmctree -ds 'burnin = 2000' -ds 'sampfreq = 1000' -ds 'nsample = 20000' \
> Potamogeton_acutifolius Spirodela_intermedia Amorphophallus_konjac Acanthochlamys_bracteata Dioscorea_alata \
> Dioscorea_rotundata Acorus_americanus Acorus_tatarinowii Tetracentron_sinense Trochodendron_aralioides \
> Buxus_austroyunnanensis Buxus_sinica Nelumbo_nucifera Telopea_speciosissima Protea_cynaroides Sarracenia_purpurea

2024-06-16 12:50:03 INFO     This is wgd v2.0.38                                                                                                                      cli.py:34
                    INFO     Checking cores and threads...                                                                                                           core.py:35
                    INFO     The number of logical CPUs/Hyper Threading in the system: 32                                                                            core.py:36
                    INFO     The number of physical cores in the system: 32                                                                                          core.py:37
                    INFO     The number of actually usable CPUs in the system: 12                                                                                    core.py:38
                    INFO     Checking memory...                                                                                                                      core.py:40
                    INFO     Total physical memory: 125.5488 GB                                                                                                      core.py:41
                    INFO     Available memory: 111.9655 GB                                                                                                           core.py:42
                    INFO     Free memory: 100.7363 GB                                                                                                                core.py:43

2024-06-16 12:54:14 INFO     tmpdir = wgdtmp_c20d4cc5-66ec-4711-b1e8-4bd3415fc045 for Potamogeton_acutifolius                                                   cli.py:240
2024-06-16 12:54:15 INFO     tmpdir = wgdtmp_57b79f1f-96e9-4d65-98b9-32c6a42e3281 for Spirodela_intermedia                                                           cli.py:240
                    INFO     tmpdir = wgdtmp_788ee945-32b9-4885-a09d-e0d7d6751eef for Amorphophallus_konjac                                                          cli.py:240
                    INFO     tmpdir = wgdtmp_3be61e0e-9695-4ee7-aa47-5069e9b25b53 for Acanthochlamys_bracteata                                                       cli.py:240
                    INFO     tmpdir = wgdtmp_17914199-b497-4a57-b166-59627eed526a for Dioscorea_alata                                                                cli.py:240
                    INFO     tmpdir = wgdtmp_b2218966-243d-4527-adba-ecad777aed52 for Dioscorea_rotundata                                                            cli.py:240
                    INFO     tmpdir = wgdtmp_18079ca0-0b92-4005-8aab-824614b1a798 for Acorus_americanus                                                              cli.py:240
                    INFO     tmpdir = wgdtmp_78b0cd3d-26c4-439f-8476-3881570afbcf for Acorus_tatarinowii                                                             cli.py:240
                    INFO     tmpdir = wgdtmp_33a5ea42-0bff-4f35-a28b-92837d428cb2 for Tetracentron_sinense                                                           cli.py:240
                    INFO     tmpdir = wgdtmp_3505e2c1-c0ec-44fe-ba4b-3f6651222dd5 for Trochodendron_aralioides                                                       cli.py:240
                    INFO     tmpdir = wgdtmp_e3e0d923-10aa-4136-8123-04b2e63a2e8a for Buxus_austroyunnanensis                                                        cli.py:240
                    INFO     tmpdir = wgdtmp_d40b87a5-294e-433c-a007-100ce950d846 for Buxus_sinica                                                                   cli.py:240
                    INFO     tmpdir = wgdtmp_ad8f14e2-12d4-46fe-b304-3458873ff9a3 for Nelumbo_nucifera                                                               cli.py:240
                    INFO     tmpdir = wgdtmp_c9ae3d52-3a35-466e-999e-9019c453b2a9 for Telopea_speciosissima                                                          cli.py:240
                    INFO     tmpdir = wgdtmp_07e310d3-4ae9-467e-a017-90c431c4c37b for Protea_cynaroides                                                              cli.py:240
                    INFO     tmpdir = wgdtmp_c03a894f-7178-4ca7-a7bd-6e37bd5a8a87 for Sarracenia_purpurea                                                            cli.py:240
                    INFO     4 threads are used for 262 gene families                                                                                                cli.py:242
                             Note that adding threads can significantly accelerate the analysis
                    INFO     Only implement protein concatenation dating via mcmctree                                                                                cli.py:244
2024-06-16 12:59:28 INFO     Running mcmctree using Hessian matrix of LG+Gamma for protein model                                                                   core.py:1048
Traceback (most recent call last):
  File "~/.conda/envs/WGD/bin/wgd", line 8, in <module>
    sys.exit(cli())
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "~y/.conda/envs/WGD/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/cli.py", line 223, in focus
    _focus(**kwargs)
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/cli.py", line 247, in _focus
    Run_MCMCTREE_concprot(Concat_paln,Concat_palnf,tmpdir,outdir,speciestree,datingset,aamodel,slist,nthreads)
  File "~y/.conda/envs/WGD/lib/python3.8/site-packages/wgd/core.py", line 1054, in Run_MCMCTREE_concprot
    McMctree.run_mcmctree(CI_table,PM_table,wgd_mrca)
  File ~/.conda/envs/WGD/lib/python3.8/site-packages/wgd/mcmctree.py", line 251, in run_mcmctree
    _run_mcmctree('mcmctree.ctrl')
  File "~/.conda/envs/WGD/lib/python3.8/site-packages/wgd/mcmctree.py", line 119, in _run_mcmctree
    sp.run(['mcmctree', control_file], stdout=sp.PIPE)
  File "~/.conda/envs/WGD/lib/python3.8/subprocess.py", line 489, in run
    with Popen(*popenargs, **kwargs) as process:
  File "~/.conda/envs/WGD/lib/python3.8/subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "~/.conda/envs/WGD/lib/python3.8/subprocess.py", line 1702, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mcmctree'

I can see the 'mcmctee' in the output file structure.

Any idea how to fix this error?

Here is the wgd_dating structure:

13:28:17    $ ls wgd_dating/
Concatenated.paln       GF00000029.paln  GF00000058.pep   GF00000088.paln  GF00000117.pep   GF00000147.paln  GF00000176.pep   GF00000206.paln  GF00000235.pep
Concatenated.paln.paml  GF00000029.pep   GF00000059.paln  GF00000088.pep   GF00000118.paln  GF00000147.pep   GF00000177.paln  GF00000206.pep   GF00000236.paln
G2S.Map                 GF00000030.paln  GF00000059.pep   GF00000089.paln  GF00000118.pep   GF00000148.paln  GF00000177.pep   GF00000207.paln  GF00000236.pep
GF00000001.paln         GF00000030.pep   GF00000060.paln  GF00000089.pep   GF00000119.paln  GF00000148.pep   GF00000178.paln  GF00000207.pep   GF00000237.paln
GF00000001.pep          GF00000031.paln  GF00000060.pep   GF00000090.paln  GF00000119.pep   GF00000149.paln  GF00000178.pep   GF00000208.paln  GF00000237.pep
GF00000002.paln         GF00000031.pep   GF00000061.paln  GF00000090.pep   GF00000120.paln  GF00000149.pep   GF00000179.paln  GF00000208.pep   GF00000238.paln
GF00000002.pep          GF00000032.paln  GF00000061.pep   GF00000091.paln  GF00000120.pep   GF00000150.paln  GF00000179.pep   GF00000209.paln  GF00000238.pep
GF00000003.paln         GF00000032.pep   GF00000062.paln  GF00000091.pep   GF00000121.paln  GF00000150.pep   GF00000180.paln  GF00000209.pep   GF00000239.paln
GF00000003.pep          GF00000033.paln  GF00000062.pep   GF00000092.paln  GF00000121.pep   GF00000151.paln  GF00000180.pep   GF00000210.paln  GF00000239.pep
GF00000004.paln         GF00000033.pep   GF00000063.paln  GF00000092.pep   GF00000122.paln  GF00000151.pep   GF00000181.paln  GF00000210.pep   GF00000240.paln
GF00000004.pep          GF00000034.paln  GF00000063.pep   GF00000093.paln  GF00000122.pep   GF00000152.paln  GF00000181.pep   GF00000211.paln  GF00000240.pep
GF00000005.paln         GF00000034.pep   GF00000064.paln  GF00000093.pep   GF00000123.paln  GF00000152.pep   GF00000182.paln  GF00000211.pep   GF00000241.paln
GF00000005.pep          GF00000035.paln  GF00000064.pep   GF00000094.paln  GF00000123.pep   GF00000153.paln  GF00000182.pep   GF00000212.paln  GF00000241.pep
GF00000006.paln         GF00000035.pep   GF00000065.paln  GF00000094.pep   GF00000124.paln  GF00000153.pep   GF00000183.paln  GF00000212.pep   GF00000242.paln
GF00000006.pep          GF00000036.paln  GF00000065.pep   GF00000095.paln  GF00000124.pep   GF00000154.paln  GF00000183.pep   GF00000213.paln  GF00000242.pep
GF00000007.paln         GF00000036.pep   GF00000066.paln  GF00000095.pep   GF00000125.paln  GF00000154.pep   GF00000184.paln  GF00000213.pep   GF00000243.paln
GF00000007.pep          GF00000037.paln  GF00000066.pep   GF00000096.paln  GF00000125.pep   GF00000155.paln  GF00000184.pep   GF00000214.paln  GF00000243.pep
GF00000008.paln         GF00000037.pep   GF00000067.paln  GF00000096.pep   GF00000126.paln  GF00000155.pep   GF00000185.paln  GF00000214.pep   GF00000244.paln
GF00000008.pep          GF00000038.paln  GF00000067.pep   GF00000097.paln  GF00000126.pep   GF00000156.paln  GF00000185.pep   GF00000215.paln  GF00000244.pep
GF00000009.paln         GF00000038.pep   GF00000068.paln  GF00000097.pep   GF00000127.paln  GF00000156.pep   GF00000186.paln  GF00000215.pep   GF00000245.paln
GF00000009.pep          GF00000039.paln  GF00000068.pep   GF00000098.paln  GF00000127.pep   GF00000157.paln  GF00000186.pep   GF00000216.paln  GF00000245.pep
GF00000010.paln         GF00000039.pep   GF00000069.paln  GF00000098.pep   GF00000128.paln  GF00000157.pep   GF00000187.paln  GF00000216.pep   GF00000246.paln
GF00000010.pep          GF00000040.paln  GF00000069.pep   GF00000099.paln  GF00000128.pep   GF00000158.paln  GF00000187.pep   GF00000217.paln  GF00000246.pep
GF00000011.paln         GF00000040.pep   GF00000070.paln  GF00000099.pep   GF00000129.paln  GF00000158.pep   GF00000188.paln  GF00000217.pep   GF00000247.paln
GF00000011.pep          GF00000041.paln  GF00000070.pep   GF00000100.paln  GF00000129.pep   GF00000159.paln  GF00000188.pep   GF00000218.paln  GF00000247.pep
GF00000012.paln         GF00000041.pep   GF00000071.paln  GF00000100.pep   GF00000130.paln  GF00000159.pep   GF00000189.paln  GF00000218.pep   GF00000248.paln
GF00000012.pep          GF00000042.paln  GF00000071.pep   GF00000101.paln  GF00000130.pep   GF00000160.paln  GF00000189.pep   GF00000219.paln  GF00000248.pep
GF00000013.paln         GF00000042.pep   GF00000072.paln  GF00000101.pep   GF00000131.paln  GF00000160.pep   GF00000190.paln  GF00000219.pep   GF00000249.paln
GF00000013.pep          GF00000043.paln  GF00000072.pep   GF00000102.paln  GF00000131.pep   GF00000161.paln  GF00000190.pep   GF00000220.paln  GF00000249.pep
GF00000014.paln         GF00000043.pep   GF00000073.paln  GF00000102.pep   GF00000132.paln  GF00000161.pep   GF00000191.paln  GF00000220.pep   GF00000250.paln
GF00000014.pep          GF00000044.paln  GF00000073.pep   GF00000103.paln  GF00000132.pep   GF00000162.paln  GF00000191.pep   GF00000221.paln  GF00000250.pep
GF00000015.paln         GF00000044.pep   GF00000074.paln  GF00000103.pep   GF00000133.paln  GF00000162.pep   GF00000192.paln  GF00000221.pep   GF00000251.paln
GF00000015.pep          GF00000045.paln  GF00000074.pep   GF00000104.paln  GF00000133.pep   GF00000163.paln  GF00000192.pep   GF00000222.paln  GF00000251.pep
GF00000016.paln         GF00000045.pep   GF00000075.paln  GF00000104.pep   GF00000134.paln  GF00000163.pep   GF00000193.paln  GF00000222.pep   GF00000252.paln
GF00000016.pep          GF00000046.paln  GF00000075.pep   GF00000105.paln  GF00000134.pep   GF00000164.paln  GF00000193.pep   GF00000223.paln  GF00000252.pep
GF00000017.paln         GF00000046.pep   GF00000076.paln  GF00000105.pep   GF00000135.paln  GF00000164.pep   GF00000194.paln  GF00000223.pep   GF00000253.paln
GF00000017.pep          GF00000047.paln  GF00000076.pep   GF00000106.paln  GF00000135.pep   GF00000165.paln  GF00000194.pep   GF00000224.paln  GF00000253.pep
GF00000018.paln         GF00000047.pep   GF00000077.paln  GF00000106.pep   GF00000136.paln  GF00000165.pep   GF00000195.paln  GF00000224.pep   GF00000254.paln
GF00000018.pep          GF00000048.paln  GF00000077.pep   GF00000107.paln  GF00000136.pep   GF00000166.paln  GF00000195.pep   GF00000225.paln  GF00000254.pep
GF00000019.paln         GF00000048.pep   GF00000078.paln  GF00000107.pep   GF00000137.paln  GF00000166.pep   GF00000196.paln  GF00000225.pep   GF00000255.paln
GF00000019.pep          GF00000049.paln  GF00000078.pep   GF00000108.paln  GF00000137.pep   GF00000167.paln  GF00000196.pep   GF00000226.paln  GF00000255.pep
GF00000020.paln         GF00000049.pep   GF00000079.paln  GF00000108.pep   GF00000138.paln  GF00000167.pep   GF00000197.paln  GF00000226.pep   GF00000256.paln
GF00000020.pep          GF00000050.paln  GF00000079.pep   GF00000109.paln  GF00000138.pep   GF00000168.paln  GF00000197.pep   GF00000227.paln  GF00000256.pep
GF00000021.paln         GF00000050.pep   GF00000080.paln  GF00000109.pep   GF00000139.paln  GF00000168.pep   GF00000198.paln  GF00000227.pep   GF00000257.paln
GF00000021.pep          GF00000051.paln  GF00000080.pep   GF00000110.paln  GF00000139.pep   GF00000169.paln  GF00000198.pep   GF00000228.paln  GF00000257.pep
GF00000022.paln         GF00000051.pep   GF00000081.paln  GF00000110.pep   GF00000140.paln  GF00000169.pep   GF00000199.paln  GF00000228.pep   GF00000258.paln
GF00000022.pep          GF00000052.paln  GF00000081.pep   GF00000111.paln  GF00000140.pep   GF00000170.paln  GF00000199.pep   GF00000229.paln  GF00000258.pep
GF00000023.paln         GF00000052.pep   GF00000082.paln  GF00000111.pep   GF00000141.paln  GF00000170.pep   GF00000200.paln  GF00000229.pep   GF00000259.paln
GF00000023.pep          GF00000053.paln  GF00000082.pep   GF00000112.paln  GF00000141.pep   GF00000171.paln  GF00000200.pep   GF00000230.paln  GF00000259.pep
GF00000024.paln         GF00000053.pep   GF00000083.paln  GF00000112.pep   GF00000142.paln  GF00000171.pep   GF00000201.paln  GF00000230.pep   GF00000260.paln
GF00000024.pep          GF00000054.paln  GF00000083.pep   GF00000113.paln  GF00000142.pep   GF00000172.paln  GF00000201.pep   GF00000231.paln  GF00000260.pep
GF00000025.paln         GF00000054.pep   GF00000084.paln  GF00000113.pep   GF00000143.paln  GF00000172.pep   GF00000202.paln  GF00000231.pep   GF00000261.paln
GF00000025.pep          GF00000055.paln  GF00000084.pep   GF00000114.paln  GF00000143.pep   GF00000173.paln  GF00000202.pep   GF00000232.paln  GF00000261.pep
GF00000026.paln         GF00000055.pep   GF00000085.paln  GF00000114.pep   GF00000144.paln  GF00000173.pep   GF00000203.paln  GF00000232.pep   GF00000262.paln
GF00000026.pep          GF00000056.paln  GF00000085.pep   GF00000115.paln  GF00000144.pep   GF00000174.paln  GF00000203.pep   GF00000233.paln  GF00000262.pep
GF00000027.paln         GF00000056.pep   GF00000086.paln  GF00000115.pep   GF00000145.paln  GF00000174.pep   GF00000204.paln  GF00000233.pep   mcmctree
GF00000027.pep          GF00000057.paln  GF00000086.pep   GF00000116.paln  GF00000145.pep   GF00000175.paln  GF00000204.pep   GF00000234.paln
GF00000028.paln         GF00000057.pep   GF00000087.paln  GF00000116.pep   GF00000146.paln  GF00000175.pep   GF00000205.paln  GF00000234.pep
GF00000028.pep          GF00000058.paln  GF00000087.pep   GF00000117.paln  GF00000146.pep   GF00000176.paln  GF00000205.pep   GF00000235.paln

Hi, it seems that mcmctree was not properly called in your run. What would you get if you type in "mcmctree" and enter?

Hey, You're right, it was a PAML installation issue. Once I fixed it, the error went away. I still can't figure out how to modify the dating-tree you provided (below) to work with my species.

17 1
((((Potamogeton_acutifolius,(Spirodela_intermedia,Amorphophallus_konjac)),(Acanthochlamys_bracteata,(Dioscorea_alata,Dioscorea_rotundata))'>0.5600<1.2863')'>0.8360<1.2863',(Acorus_americanus,Acorus_tatarinowii))'>0.8360<1.2863',((((Tetracentron_sinense,Trochodendron_aralioides),(Buxus_austroyunnanensis,Buxus_sinica))'>1.1080<1.2863',(Nelumbo_nucifera,(Telopea_speciosissima,Protea_cynaroides)))'>1.1080<1.2863',(Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2))'>1.1080<1.2863')'>1.2720<2.4720';

So I used it as is except for replacing Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2 with MySpecies_ap1,MySpecies_ap2. I got WGD a reasonable peak, which seems to be consistent with earlier evidences. but the range between the low and high 90% CI is a bit large, which worries me.

"Posterior mean for the age of wgd is 81.0112 million years ago from Concatenated peptide alignment and 95% credibility intervals (CI) is 53.2662-108.8130 million years."

from the anchored KS distribution, the mode is 0.52, and 95% CI is 0.23 - 2.19. from anchored pairs of duplications, the aggregation of duplicates age at KS = 0.72 from non-anchor pairs of duplications, the aggregation of duplicates age at KS = 0.51

When I ploted the WGD age distribution using the following command, the Median, posterior mean, and mode were 81, 80, and 84 mya. the 95% CI is 56.61-103 mya.

python $PATH/postplot.py postdis dates.txt --percentile 90 --title "WGD date" --hpd -o "WGD_date.svg"

What do you think?

There are four resultant subfolders from wgd peak, among which you can usually choose peak range from AnchorKs_FindPeak, AnchorKs_GMM or SegmentGuideKs_GMM. If the one from AnchorKs_FindPeak is too wide, you can always try the other two. Besides, a broad 95% HPD CI width reflects the constraint from fossil calibrations. The requirement of the starting tree topology is that your focal species is the only species who has experienced the WGD event to be dated in the tree. If you may find and use fossil calibrations that have narrower bounds, the concern of yours will be relieved too.

heche-psb / wgd

RE: dating tree #36