Body: <p>I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files.</p>
  <p>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.</p>
  <p>Could someone please give me some guidance on the most suitable parameters to give a good image, and comparison between the two phylogeny.</p>
  <p>please see the newick format below:</p>
  <pre><code>((((((((((((((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);
  </code></pre>
  <p>And a link to the tree viewer:</p>
  <p><a href="https://eti.pg.edu.pl/treecmp/WEB" rel="nofollow noreferrer">https://eti.pg.edu.pl/treecmp/WEB</a></p>
  <hr />
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T18:15:49.080Z
Comments.Text: These are also rooted on the Wuhan reference genome
Comments.UserDisplayName: Theo Jones
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T19:52:53.427Z
Comments.Text: Interesting, will be at least until the weekend before I can respond
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T21:23:31.530Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T21:29:23.767Z
Comments.Text: This is for an undergraduate dissertation, so I mean it doesn’t need to be crazy in depth analysis. Due to the pandemic, we’ve been forced away from wet lab work. So my main issue is having to self teach so much new analytic methods. So just the basic parameters, on how one would get the most out of the programme... or failing that another programme with less in depth parameters
Comments.UserDisplayName: Theo Jones
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T21:34:03.250Z
Comments.Text: Okay you've just made my "when I get around to doing it" that bit more "when I get around to doing it". Still its an interesting approach and it is a topical paper for sure.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-17T21:38:23.300Z
Comments.Text: I don’t know whether I should take that as positive or negative? :D
Comments.UserDisplayName: Theo Jones
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-24T12:57:43.750Z
Comments.Text: Hi @TheoJones I'll do this over next weekend, apologies for the delay.
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny><covid-19><sars-cov-2><homework>
Title: Comparison of phylogeny of SARS2 whole genome vs spike genome
ThreadText: # Comparison of phylogeny of SARS2 whole genome vs spike genome
  
  (Asked by: username_0 on 2020-11-17)
  
  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.
  
  **Tags:** phylogenetics, phylogeny, covid-19, sars-cov-2, homework
  
  > **Comments:**
  > **username_0**: These are also rooted on the Wuhan reference genome  
  > **username_1**: Interesting, will be at least until the weekend before I can respond  
  > **username_1**: 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.  
  > **username_0**: This is for an undergraduate dissertation, so I mean it doesn’t need to be crazy in depth analysis. Due to the pandemic, we’ve been forced away from wet lab work. So my main issue is having to self teach so much new analytic methods. So just the basic parameters, on how one would get the most out of the programme... or failing that another programme with less in depth parameters  
  > **username_1**: Okay you've just made my "when I get around to doing it" that bit more "when I get around to doing it". Still its an interesting approach and it is a topical paper for sure.  
  > **username_0**: I don’t know whether I should take that as positive or negative? :D  
  > **username_1**: Hi @username_0 I'll do this over next weekend, apologies for the delay.  
  
  ---
  
  ## 0 answers
  
  