Hi everyone,
I am a Ph.D. student and work in the field of parasitology. I regularly use molecular techniques and would like to approach phylogenetic trees. More specifically, recently, I have worked on the microscopical identification of an insect which has been confirmed by conventional PCR and sequencing. Reached this point, I would like to go more into depth and create a phylogenetic tree (a fairly uncomplicated one in which I would compare a limited number of sequences 5-6 c.ca). I don’t have extensive experience with this; therefore, I was looking for a manageable software for beginners possibly free and with some official tutorials available online.
Thank you to everyone who will join the discussion and bring their expertise and experience around the table.
Cheers!
Alessandra
Hi!
I strongly recommend MEGA for the beginners.
Google it as mega software.
Cheers!
Kaan Hürkan I was using MEGA for the last two years. But nowadays I'm facing some problems. It shows the RAM issue. But I used it before without any problem. I have tried different laptops and desktop having a large RAM facility.
(Some full genome sequence (n=26) was included and each of them contains about 162131 bp).
How can i solve?
I would recommend BEAST v1.
https://beast.community
The package includes one software to set your sequences up for analysis (BEAUTi), one for running the analyses (BEAST), one for assembling the phylogenetic tree (TreeAnnotator) and one to visualize the tree (FigTree). There is a bit of a learning threshold, but once you know how to set up BEAUTi, the rest is quite easy, and your results are professional. There is a good manual, and a forum to ask questions if you get stuck.
PAUP and MEGA are the best. I have also used CLUSTAL W Online (https://www.genome.jp/tools-bin/clustalw ) for making trees. You may try any of these.
Best of Luck
The MEGA program is a simple program with a good UI. Other recommendations are PAUP and PHYLIP.
These programs have advantages and disadvantages, we can choose based on the approach and algorithm model that we want to use
Thanks everyone for joining the discussion and your helpful tips!
MEGA is probably the easiest way in if you have a single-marker dataset. If you are working on a multi-gene dataset, you should probably infer the best partitioning scheme and best evolutionary model for each partition, for which PhyloSuite may be a more suitable tool (it incorporates IQ-TREE ML and MrBayes BI): https://dongzhang0725.github.io/
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