Hi Laura,

as the name suggest, to do a phylogenetic tree you will always need genes.

So, yes, you can definitely generate a phylogenetic tree from your nucleotide sequences or you can check a database entering the name of your families and genera and obtain additional nucleotide sequences from there. For example, you can check Genbank (https://www.ncbi.nlm.nih.gov/genbank/?), enter the genus name you are looking for, select one of the (probably) many results you will obtain, and download the nucleotide sequences that better suits you.

If you already have nucleotide sequences of the same gene (for example Cytochrome Oxidase, COI) from each of your families or genera, you can easily generate a phylogenetic tree using the free software MEGA. You can download MEGA from here: https://www.megasoftware.net/.

Firstly, you will have to make an alignment of your nucleotide sequences.

Align -> edit/build alignment -> create new alignment -> select DNA or Protein

At this point you can simply copy/paste your sequences from the FASTA format into your alignment. Once you have all the sequences pasted, you have to align them (clicking on the button "W") and select what model you want to adopt for this (such as Kimura-2-Parameter, K2P). Once the sequences are aligned you can proceed an select the best algorithm to build your phylogenetic tree. You may want to try multiple algorithm, maybe, such as Neighbor Joining (NJ) or Maximum Likelihood (ML). There are plenty of sources online explaining what are the differences and when it is better to use a certain model/algorithm or another.

Keep in mind that different genes have different "resolutions". This means that if you want a phylogenetic tree of different families, you will probably need a gene very conserved (maybe a nuclear gene?), while if you are looking at different species, you will need a gene that mutates at a quicker rate (like COI).

Hope this helps!

Feel free to ask additional questions and/or be a bit more specific (e.g. what nucleotide sequences do you have? what organisms are we talking about? Bacteria, insects, humans?)

Ofcourse, you can build the tree with amino acid sequence. You can do it online. Use any multiple sequence aligner and use the alignment to make phylogenetic tree. All can be done using http://www.phylogeny.fr/

The other thing what you asked, could also be possible but it needs some tricks and quite good bioinformatics understanding.

In addition to the above, I would definitely try a software we have been utilising in the past: MEGAN, available at http://ab.inf.uni-tuebingen.de/software/megan6/

This software is meant for (shotgun) metagenomic visualisation and analysis. Please also check https://www.mg-rast.org