tree with selected species

Question

[dimitrischat]

Hello, is there a way to do a phylogeny tree using selected species? I used this link https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi, in order to get phylip data and then which program do you suggest, also wanna show million years for the evolution. But i also wanted to know if there is an online tool to do the whole process on that tool. Thanks

[Joe]

It is non-trivial to show evolution in units of time without accurate molecular clocks and/or ancestral sequences. You could look at a tool like BEAST for this, but be aware that it is not as simple as just chucking sequences at it if you want the numbers you get to be remotely realistic.

[dimitrischat]

dont want chuck sequences in any tool. Just wanna show the evolution between my desired species. Thats all

[Joe]

Right, but how do you propose to do that without using a tool to apply some sort of evolutionary model to it?

[Mehmet]

For phylogeny there are many tools. some of them are : RAxML IQ-TREE2 PAUP Phylobayes MrBayes

for divergence time analyses (million years as you wrote) you can youse BEAST tool as @Joe said, but you need to know molecular clocks. For this you can read manuscripts and can have an idea about molecular clocks of your species of interest.

[dimitrischat]

data i got from ncbi is like this :

(
(
(
(
(
'Rattus norvegicus':4,
'Mus musculus':4
)Muridae:4,
(
'Felis catus':4,
'Canis lupus':4
)Carnivora:4,
(
'Homo sapiens':4,
'Pan troglodytes':4
)Hominidae:4
)Mammalia:4,
'Danio rerio':4
)Chordata:4,
'Drosophila melanogaster':4,
'Caenorhabditis elegans':4
)Metazoa:4,
'Zea mays':4
)Eukaryota:4;

phylip format

[dimitrischat]

txt is like this

Eukaryota

+-Metazoa

| +-Chordata

| | +-Mammalia

| | | +-Rodentia

| | | | \-Muridae

| | | |   +-Rattus

| | | |   | \-Rattus norvegicus

| | | |   \-Mus

| | | |     \-Mus musculus

| | | +-Carnivora

| | | | ++Felidae

| | | | | \-Felis catus

| | | | \+Canidae

| | | |   \-Canis lupus

| | | \-Primates

| | |   \-Hominidae

| | |     +-Homo

| | |     | \-Homo sapiens

| | |     \-Pan

| | |       \-Pan troglodytes

| | \+Actinopteri

| |   \-Danio rerio

| ++Arthropoda

| | \-Drosophila melanogaster

| \+Nematoda

|   \-Caenorhabditis elegans

\+Viridiplantae

  \-Zea mays

-----------------------------------

[Joe]

There is no way to infer evolutionary divergence dates from that data, there's no molecular information. The best you could do is a literature review to find out when other papers proposed the evolutionary splits happen.