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Thread subject: Questions about the evaluation 1

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Questions about the evaluation 1
trungbui
6 Feb 2017 11:12
Non evaluated contribution

Dear teacher,

Thanks for your evaluation, it's very specific and I will continue correct my work.

I have a question, I hope that you will help me to make it more clear to finish my cart.

I have to trees for classification this ORF, they are located in the Raw Result as below. You commented that "- I don't understand your phylogenetic trees : you write in the taxonomic report analysis that the outgoup is BETAPROTEOBACTERIA. And you did not select a sequence from the outgroup so your tree is completely wrong ! Redo ti with the outgroup sequences." Did you just see the first tree in Fig.1? The last tree I want to choose is in the Fig.2.

Fig. 1: Phylogeny.fr tree of In Group and Outgroup are selected in Bacteria:Proteobacteria:Gammaproteobacteria

                                +--BPGAPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)
                                +-+
                                | +-BPGAPP3_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
                              +-+
                           +--+ +--BPGAPP4_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada       (Ingroup)
                           |  |
          +----------------+  +-BPGAPP5_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada          (Ingroup)
          |                |
          |                +----BPGAPP6_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada         (Ingroup)
          |
 +--------+
 |        |  +----------------BPGAPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
 |        |  |
 |        +--+  +--------------------------BPGAII1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada   (Ingroup)
 |           |  |
 |           |  |          +---------BPGAAG1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada       (Ingroup)
 |           +--++---------+
 |              ||         |      +-----BPGAAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
 |              ||         +------+
 |              ++                +-----BPGAAA2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)
 |               |
 |               |   +-----------------BPGACC1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada        (Ingroup)
 |               |   |
 |               +---+              +----BPGASS1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada       (Ingroup)
 |                   +--------------+
 |                                  +-----BPGASS2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
 |
 |    +-----------------------------------BPGOAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril    (Outgroup)
 |    |
 |    |         +-------BPGAAM3_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
 |    |         |
 |    |   +-----+
 +----+   |     |  +-------BPGAAM4_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
      |   |     +--+
      |   |        +-------BPGAAM5_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)
      |   | 
      |   |         +---------BPGOHS1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril     (Outgroup)
      +---+ +-------+
          | |       |   +----------BPGOHH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril    (Outgroup)
          | |       +---+
          | |           +-----BPGOHH2_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril     (Outgroup)
          | |
          +-+     +----------------BPGOHE1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril    (Outgroup)
            |  +--+
            |  |  +-------------------BPGOH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirill   (Outgroup)
            |  |
            |  |       +---------------BPGOOO2_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril    (Outgroup)
            +--+ +-----+
               | |     +----------BPGAAM2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
               | |
               +-++------------------BPGOM1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirill    (Outgroup)
                 ||
                 ||
                 ||            +------BPGOOO1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril     (Outgroup)
                 ++   +--------+
                  |   |        +---BPGOO1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirill      (Outgroup)
                  |   |
                  +---+            +-----------------------------------TO36D_6155080_Translation_18-1010_indirect_strand
                      |      +-----+
                      +------+     +------------BPGAAM1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
                             |
                             +----------------BPGAAG2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)


Fig. 2a- PhylML: Phylogeny.fr tree of In Group and Outgroup are selected in Bacteria:Proteobacteria

 
                  +-------------------------------------BPG1_Bacteria_Proteobacteria_Gammaproteobacteria_E-value=2e-55_B   (Ingroup)
                  |
                  |+----------------------------BPGOAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril       (Ingroup)
                  ||
                  ||                 +-----------------BPGOH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirill    (Ingroup)
          +-------+|         +-------+
          |       ||         |       +----------------BPGOHH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril       (Ingroup)
          |       ||       +-+  
          |       ||       | +-------------------BPGAAM1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)
          |       ||       |
          |       ++       |         +-----BPGPPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada       (Ingroup)
          |        |   +---+         |
          |        |   |   |         |
          |        |   |   |         |      +---BPGPPP5_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
          |        |   |   |         |    +-+
          |        |   |   +---------+    | | +-BPGPPP4_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
          |        |   |             |  +-+ +-+
          |        |   |             |  | |   +---BPGPPP3_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
          |        +---+             |  | |
          |            |             +--+ +--BPGPPP6_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada        (Ingroup)
          |            |                |
       +--+            |                +---BPGPPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada         (Ingroup)
       |  |            |
       |  |            |    +--------------------------------------TO36D_6155080_Translation_18-1010_indirect_strand
       |  |            |    |
       |  |            +----+              +-BPGPMA1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada     (Ingroup)
       |  |                 +--------------+
       |  |                                +-BPGPMA2_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada     (Ingroup)
       |  |
       |  |                                +-BPGAPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada      (Ingroup)
       |  |           +--------------------+
       |  |           |                    +-----BPGAPP3_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
       |  |      +----+
       |  |      |    +----------------BPGAPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada       (Ingroup)
       |  |      |
 +-----+  |      |               +------BPGEEE3_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter     (Ingroup)
 |     |  |      |               |
 |     |  +------+              ++
 |     |         |              |+----BPGEEB1_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter       (Ingroup)
 |     |         |   +----------+
 |     |         |   |          |   +---BPGEEE1_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter      (Ingroup)
 |     |         |   |          +---+
 |     |         +---+              +--BPGEEE2_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter       (Ingroup)
 |     |             |
 |     |             |       +---------------BPGAAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
 |     |             +-------+
 |     |                     +---------------------BPGASS1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada     (Ingroup)
 |     |
 |     |    +-------------------------------BPGXXL1_Bacteria_Proteobacteria_Gammaproteobacteria_Xanthomonada      (Ingroup)
 |     +----+
 |          +---------------BPGMM1_Bacteria_Proteobacteria_Gammaproteobacteria_Methylococcal    (Ingroup)
 |
 |                  +--------------BPBNNE1_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales    (Outgroup)
 |                  |
 |     +------------+    +-BPBNNN3_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales     (Outgroup)
 |     |            |    |
 |     |            +----++-BPBNNN1_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales    (Outgroup)
 |     |                 ++
 |     |                  +-BPBNNN2_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales   (Outgroup)
 |     |
 +-----+
       |         +--------------BPBBAP1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial    (Outgroup)
       |     +---+
       |     |   |    +----------------BPBBBP1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial    (Outgroup)
       |     |   +----+
       +-----+        +-----------BPBBBB1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial   (Outgroup)
             |
             |   +-----------BPB1_Bacteria_Proteobacteria_Betaproteobacteria_E-value=2e-54_Ba    (Outgroup)
             +---+
                 | +--------BPBBCX1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial (Outgroup)
                 +-+
                   +-----BPBBCC1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial   (Outgroup)

Fig.2b) BioNJ- PhylML: Phylogeny.fr tree of In Group and Outgroup are selected in Bacteria:Proteobacteria   (Outgroup)

  
       +-----------------------------BPGAAM1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada   (Ingroup)
       |
     +-+             +---------BPGPPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
     | |             |
     | |             |    +----BPGPPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada  (Ingroup)
     | +-------------+   ++
     |               |   |+------BPGPPP6_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
     |               |   |
     |               +---+  +---BPGPPP3_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada   (Ingroup)
    ++                   |  |
    ||                   +--++---BPGPPP4_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada   (Ingroup)
    ||                      ++
    ||                       |
    ||                       +-----BPGPPP5_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada    (Ingroup)
    ||
  +-+|    +-----------------------BPGOH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirill   (Ingroup)
  | |+----+
  | |     +----------------------BPGOHH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril    (Ingroup)
  | |
  | | +-------------------------------------------------TO36D_6155080_Translation_18-1010_indirect_strand 
 ++ +-+
 ||   |                       +--BPGPMA1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada  (Ingroup)
 ||   +-----------------------+
 ||                           +--BPGPMA2_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada  (Ingroup)
 ||
 ||+------------------------------------------------BPG1_Bacteria_Proteobacteria_Gammaproteobacteria_E-value=2e-55_B   (Ingroup)
 |++
 | +------------------------------------BPGOAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril   (Ingroup)
 |
 |                                               +----BPGAPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada (Ingroup)
 |                 +-----------------------------+
 |                 |                             +------BPGAPP3_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada   (Ingroup)
 |            +----+
 |            |    +-------------------------BPGAPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
 |            |
 |            |                    +----BPGEEE1_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter  (Ingroup)
 |            |                    |
 |    +-------+                 +--+
 |    |       |                ++  +----BPGEEE2_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter   (Ingroup)
 |    |       |                ||
 |    |       |+---------------++-------BPGEEB1_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter  (Ingroup)
 |    |       ||               |
 |    |       ++               +----------BPGEEE3_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter    (Ingroup)
 |    |        |
 |    |        |  +-------------------------BPGAAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
 |    |        +--+
 +----+           +---------------------------BPGASS1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada    (Ingroup)
      |
      |     +---------------------------------------BPGXXL1_Bacteria_Proteobacteria_Gammaproteobacteria_Xanthomonada  (Ingroup)
      |  +--+
      |  |  +---------------------------BPGMM1_Bacteria_Proteobacteria_Gammaproteobacteria_Methylococcal    (Ingroup)
      |  |
      |  |                      +------------------BPBNNE1_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales   (Outgroup)
      |  |                      |
      |  |        +-------------+            +--BPBNNN3_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales   (Outgroup)
      +--+        |             |            |
         |        |             +------------+ +-BPBNNN1_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales    (Outgroup)
         |        |                          +-+
         |        |                            +BPBNNN2_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales    (Outgroup)
         |        |
         +--------+
                  |     +----------------------BPBBAP1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial    (Outgroup)
                  |  +--+
                  |  |  |   +-----------------BPB1_Bacteria_Proteobacteria_Betaproteobacteria_E-value=2e-54_Ba    (Outgroup)
                  |  |  +---+
                  |  |      |    +------------BPBBCX1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial     (Outgroup)
                  +--+      +----+
                     |           +---------BPBBCC1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial     (Outgroup)
                     |
                     |+-------------------------BPBBBP1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial (Outgroup)
                     ++ 
                      +---------------------BPBBBB1_Bacteria_Proteobacteria_Betaproteobacteria_Burkholderial     (Outgroup)