If you are willing to consider other options than R, I would suggest using needle or needleall from EMBOSS. This does a global pairwise alignment using Needleman-Wunsch algorithm for sequence sets and reports global sequence similarity and identity between two sequences. Both these programs take two input sequence files.

If you want to compare a sequence from your species of interest against each of its orthologs, use needle. Create a file with the sequence from your species of interest and another file with its ortholog sequences.

If you also want to compare the orthologs sequences among themselves (all-against-all), use needleall. Create a multi-FASTA file of all sequences belonging to a single orthologous group and use the same file as the two input sequences. There might be redundant comparisons (seq1 vs seq2 and seq2 vs seq1).

Just a friendly suggestion about terminologies ("true orthologues"). We cannot infer homology from sequence-similarity based methods such as BLAST (inParanoid uses BLAST). The best we can call the hits as putative homologs. We need to do phylogenetic analyses to talk about homology.