WARNING closely-related and very-long sequences

[ireneortega]

I run the command:
FastTree -nt -gtr core_gene_alignment.aln > core_genome_aln.newick
and printed the following warnings:

FastTree Version 2.1.11 Double precision (No SSE3)
Alignment: core_gene_alignment.aln
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
Initial topology in 94.44 seconds of    119    1 of    122 seqs    100)   
Refining topology: 28 rounds ME-NNIs, 2 rounds ME-SPRs, 14 rounds ML-NNIs
Total branch-length 0.116 after 925.62 sec 101 of 120 splits, 0 changes   x delta 0.000)    

WARNING! This alignment consists of closely-related and very-long sequences.
WARNING! FastTree (or other standard maximum-likelihood tools)
may not be appropriate for aligments of very closely-related sequences
like this one, as FastTree does not account for recombination or gene conversion
...

Should I be worried that the tree is not correct? How can I solve them within FastTree? Thanks!

[Eirwyn-sheen]

I also encounter this problem. My fasttree version is 2.1.10.