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)