You don't need a server to reconstruct phylogeny. CSI Phylogeny is basically BWA + SAMtools. You can create a similar custom pipeline on HPC or a local machine and process as many isolates as you want.

Thank you for your answer. I fully agree that is it entirely possible to do it. However, an online server usually make easy the work for who is not bioinformatician, like me.

http://www.atgc-montpellier.fr/phyml/

http://iqtree.cibiv.univie.ac.at/

https://raxml-ng.vital-it.ch/#/

https://ngphylogeny.fr/

http://www.trex.uqam.ca/index.php?action=raxml&project=trex

Good luck!

Jose Alberto Lopez-Aleman That's a very useful information. Appreciate your response.

The CIPRES Science Gateway (phylo.org) has several options for running phylogenetic analyses online, and is free for users below a certain threshold of computational time.