1
$\begingroup$

I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files.

My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent within the spike, or as a global event across the whole genome. In order to do this I have chosen to use VisualTreeCMP. However, when it comes to choosing how to compare these I am very confused by all the possible options.

Could someone please give me some guidance on the most suitable parameters to give a good image, and comparison between the two phylogeny.

please see the newick format below:

((((((((((((((hCoV-19/Scotland/CVR140/2020|EPI_ISL_425684|2020-03-16:0.00026192,hCoV-19/England/CAMB-73211/2020|EPI_ISL_440287|2020-03-21:0.00026198):0.00000084,hCoV-19/Wuhan/HBCDC-HB-06/2020|EPI_ISL_412982|2020-02-07:0.00000000):0.00000034,hCoV-19/Gambia/NPHL-287/2020|EPI_ISL_561300|2020:0.00000000):0.00000372,hCoV-19/England/NORT-286167/2020|EPI_ISL_573313|2020-07-21:0.00025782):0.00002652,(hCoV-19/South_Africa/KRISP-0543/2020|EPI_ISL_498084|2020-07-12:0.00020599,(hCoV-19/England/ALDP-49EC3C/2020|EPI_ISL_559586|2020-05-20:0.00027741,hCoV-19/Belgium/HCM-0324151/2020|EPI_ISL_420408|2020-03-24:0.00024635):0.00005585):0.00021443):0.00002118,(hCoV-19/Colombia/MAG-INS-87968/2020|EPI_ISL_498152|2020-03-25:0.00015372,((hCoV-19/Australia/VIC8930/2020|EPI_ISL_565286|2020-07-29:0.00000000,hCoV-19/Australia/VIC8929/2020|EPI_ISL_565285|2020-07-28:0.00000000):0.00047159,(hCoV-19/Australia/VIC5819/2020|EPI_ISL_518613|2020-07-20:0.00024688,(hCoV-19/Australia/VIC4715/2020|EPI_ISL_519103|2020:0.00000000,hCoV-19/Australia/VIC2165/2020|EPI_ISL_480772|2020-03-19:0.00000000):0.00001495):0.00004719):0.00036022):0.00009570):0.00004876,((((hCoV-19/Wales/PHWC-16BD74/2020|EPI_ISL_573970|2020-09-15:0.00058675,hCoV-19/Spain/PV-IBV-001568/2020|EPI_ISL_467121|2020-03-13:0.00000000):0.00015901,hCoV-19/England/CAMB-7AAD6/2020|EPI_ISL_433837|2020-04-07:0.00009990):0.00003774,hCoV-19/Greece/HPI-6465/2020|EPI_ISL_451311|2020-03-29:0.00009055):0.00010675,((hCoV-19/USA/CA-SR0097/2020|EPI_ISL_445096|2020-03-13:0.00026193,hCoV-19/Iceland/13/2020|EPI_ISL_417765|2020-02-27:0.00026193):0.00020549,(hCoV-19/England/LIVE-A4CDD/2020|EPI_ISL_500083|2020-03-12:0.00007450,(hCoV-19/Wales/PHWC-16C441/2020|EPI_ISL_574056|2020-09-19:0.00022387,hCoV-19/England/SHEF-10B2F49/2020|EPI_ISL_537266|2020-05-21:0.00003797):0.00018736):0.00008143):0.00010981):0.00001973):0.00006712,(hCoV-19/Italy/LOM-UniMI-L134/2020|EPI_ISL_542130|2020-03-17:0.00064152,hCoV-19/Hong_Kong/HKU-200823-001/2020|EPI_ISL_516798|2020-03-26:0.00015299):0.00016120):0.00001351,(hCoV-19/USA/TX-HMH-1807/2020|EPI_ISL_542855|2020-04-20:0.00010829,hCoV-19/USA/CA-ALSR-1462/2020|EPI_ISL_494618|2020-03-20:0.00015349):0.00017136):0.00008773,(hCoV-19/USA/MA-MGH-00617/2020|EPI_ISL_460393|2020-03-28:0.00022036,(hCoV-19/USA/WA-S28/2020|EPI_ISL_417081|2020-03-02:0.00000726,hCoV-19/Singapore/746/2020|EPI_ISL_500560|2020-07-08:0.00025453):0.00022704):0.00003603):0.00001521,(hCoV-19/Spain/MD-IBV-006433/2020|EPI_ISL_510145|2020-04-03:0.00030013,hCoV-19/Austria/CeMM0009/2020|EPI_ISL_419662|2020-03-14:0.00000000):0.00025838):0.00001169,hCoV-19/Wuhan/IME-WH01/2020|EPI_ISL_529213|2019-12-30:0.00000000):0.00000016,hCoV-19/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123|2019-12-24:0.00000000):0.00000045,hCoV-19/USA/WA-S106/2020|EPI_ISL_417159|2020-02-29:0.00026265,NC_045512.2_Severe_acute_respiratory_syndrome_coronavirus_2_isolate_Wuhan-Hu-1_complete_genome:0.00000000);

(((((((((((hCoV-19/England/ALDP-49EC3C/2020|EPI_ISL_559586|2020-05-20:0.00013635,hCoV-19/Belgium/HCM-0324151/2020|EPI_ISL_420408|2020-03-24:0.00006529):0.00000773,hCoV-19/South_Africa/KRISP-0543/2020|EPI_ISL_498084|2020-07-12:0.00026099):0.00013025,(hCoV-19/England/LIVE-A4CDD/2020|EPI_ISL_500083|2020-03-12:0.00016259,(hCoV-19/Gambia/NPHL-287/2020|EPI_ISL_561300|2020:0.00016807,hCoV-19/England/CAMB-73211/2020|EPI_ISL_440287|2020-03-21:0.00013706):0.00000534):0.00000008):0.00000278,(hCoV-19/England/NORT-286167/2020|EPI_ISL_573313|2020-07-21:0.00036517,((hCoV-19/Australia/VIC8930/2020|EPI_ISL_565286|2020-07-29:0.00000000,hCoV-19/Australia/VIC8929/2020|EPI_ISL_565285|2020-07-28:0.00000012):0.00009405,(hCoV-19/Australia/VIC5819/2020|EPI_ISL_518613|2020-07-20:0.00006516,(hCoV-19/Australia/VIC4715/2020|EPI_ISL_519103|2020:0.00003344,hCoV-19/Australia/VIC2165/2020|EPI_ISL_480772|2020-03-19:0.00003367):0.00000193):0.00000601):0.00017105):0.00002318):0.00000716,hCoV-19/Greece/HPI-6465/2020|EPI_ISL_451311|2020-03-29:0.00004599):0.00008629,(hCoV-19/England/SHEF-10B2F49/2020|EPI_ISL_537266|2020-05-21:0.00015654,(hCoV-19/Wales/PHWC-16C441/2020|EPI_ISL_574056|2020-09-19:0.00019758,hCoV-19/Wales/PHWC-16BD74/2020|EPI_ISL_573970|2020-09-15:0.00023814):0.00021545):0.00003087):0.00000571,((hCoV-19/USA/TX-HMH-1807/2020|EPI_ISL_542855|2020-04-20:0.00023928,hCoV-19/Colombia/MAG-INS-87968/2020|EPI_ISL_498152|2020-03-25:0.00013017):0.00003266,(hCoV-19/Scotland/CVR140/2020|EPI_ISL_425684|2020-03-16:0.00003644,hCoV-19/Italy/LOM-UniMI-L134/2020|EPI_ISL_542130|2020-03-17:0.00023391):0.00000153):0.00000121):0.00012657,(hCoV-19/Singapore/746/2020|EPI_ISL_500560|2020-07-08:0.00034258,(hCoV-19/Iceland/13/2020|EPI_ISL_417765|2020-02-27:0.00012787,(hCoV-19/England/CAMB-7AAD6/2020|EPI_ISL_433837|2020-04-07:0.00012752,(hCoV-19/USA/CA-ALSR-1462/2020|EPI_ISL_494618|2020-03-20:0.00010172,hCoV-19/Hong_Kong/HKU-200823-001/2020|EPI_ISL_516798|2020-03-26:0.00020057):0.00000680):0.00004213):0.00002475):0.00002767):0.00000390,(hCoV-19/Wuhan/HBCDC-HB-06/2020|EPI_ISL_412982|2020-02-07:0.00007999,(hCoV-19/Spain/PV-IBV-001568/2020|EPI_ISL_467121|2020-03-13:0.00019054,((hCoV-19/Wuhan/IME-WH01/2020|EPI_ISL_529213|2019-12-30:0.00003592,hCoV-19/Spain/MD-IBV-006433/2020|EPI_ISL_510145|2020-04-03:0.00020087):0.00000317,(hCoV-19/USA/CA-SR0097/2020|EPI_ISL_445096|2020-03-13:0.00011733,(hCoV-19/USA/MA-MGH-00617/2020|EPI_ISL_460393|2020-03-28:0.00013271,(hCoV-19/USA/WA-S28/2020|EPI_ISL_417081|2020-03-02:0.00003240,hCoV-19/USA/WA-S106/2020|EPI_ISL_417159|2020-02-29:0.00006806):0.00001270):0.00000336):0.00008627):0.00001038):0.00001150):0.00004587):0.00000335,hCoV-19/Austria/CeMM0009/2020|EPI_ISL_419662|2020-03-14:0.00013033):0.00000452,hCoV-19/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123|2019-12-24:0.00010072,NC_045512.2_Severe_acute_respiratory_syndrome_coronavirus_2_isolate_Wuhan-Hu-1_complete_genome:0.00000000);

And a link to the tree viewer:

https://eti.pg.edu.pl/treecmp/WEB


I am just requesting the basic parameters, on how one would get the most out of the programme... or failing that another programme with less in depth parameterization.

$\endgroup$
7
  • $\begingroup$ These are also rooted on the Wuhan reference genome $\endgroup$
    – Theo Jones
    Nov 17 '20 at 18:15
  • $\begingroup$ Interesting, will be at least until the weekend before I can respond $\endgroup$
    – M__
    Nov 17 '20 at 19:52
  • $\begingroup$ You need a variety of metrics in context, but like ... hmmmm, you're expecting a lot from a single tree comparison tool, albeit its parameter rich. $\endgroup$
    – M__
    Nov 17 '20 at 21:23
  • 1
    $\begingroup$ I don’t know whether I should take that as positive or negative? :D $\endgroup$
    – Theo Jones
    Nov 17 '20 at 21:38
  • 1
    $\begingroup$ Hi @TheoJones I'll do this over next weekend, apologies for the delay. $\endgroup$
    – M__
    Nov 24 '20 at 12:57

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.