tl;dr; I wonder , is there any known tool / webserver / r package to check quality of MSA?
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The idea here is, for a given protein sequence to find out set of orthologues and perform the phylogenetic analysis. To do so, I performed blast and got first set of orthologues. However, to get complete set of orthologues I performed multiple blast with different start seed. At the end I combined all the confident (evalue <= 0.00001, qcov =90%, % identity = 40 %) blast hits. Next, I performed MSA. Now, I want to check whether given MSA is confident and represent set of orthologues for a given query protein.