Secondly, amino substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. (or to align)?

link to this sentence .

If it were to be "to align," is the meaning changed?

Consider the to-infinitive pattern when it acts as a modifer of noun.

I have something to do.

Well, if want to follow my Indonesian logic I will write like the first sentence above, like

I have something to be done.

Somebody, help me!!!! This grammar really messes me up.

to-inf or to be verb III???
The to + base verb is an infinitive in active voice.

The to + be + past participle is the infinitive in passive voice.

I have something to do. -> I will do it myself. No one else will do it.

I have something to be done. -> I will ask someone else to do it. It does leave open the possibility that I will do it, but who does it is not important.

The dogs are waiting to be fed. -> Someone will feed the dogs. They will not feed themselves.

The dogs are waiting to eat. -> The dogs will do the eating.

The food is waiting to be eaten. -> Someone will eat the food. The food is just sitting there on the table.

I hope this helps. The sentence you gave about the amino substitution matrices is too technical for me to decipher and explain. However, there will be a difference in the active versus passive voice infinitive.
rivosuothSecondly, amino substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. (or to align)?
...
If it were to be "to align," is the meaning changed?
Yes and no. You can argue that the meaning is not changed, but to be aligned is still the better choice in my opinion, because the tone is different. You have something (the sequences) and a procedure called alignment is going to be performed on them, so they are the sequences to be aligned. It's the same pattern as:

Here are the apples to be washed.

Here are the documents to be copied.

Here are the numbers to be added.

The impression here is that the procedure of washing, or copying, or adding is an already established procedure, that the focus is on the procedure, and the apples, the documents, and the numbers are (more or less) 'lined up and waiting' to undergo this procedure.

_______________

We can change them like this:

Here are the apples to wash.

Here are the documents to copy.

Here are the numbers to add.

But now the focus is on the person who has to do these things. These are almost imperatives: Wash these apples! Copy these documents! Add these numbers!

I don't think that that is the correct tone to take in a professional scientific paper.

CJ
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rivosuothConsider the to-infinitive pattern when it acts as a modifer of noun.
I have something to do.
Well, if want to follow my Indonesian logic I will write like the first sentence above, like
I have something to be done.
As explained above, the two have similar meanings. (By the way, Indonesian logic may not work for English grammar. Sometimes not even English logic works for English grammar!)

I have something to do ~ I have something that I have to do. ~ There is something for me to do.

In this case we native speakers would not think of it as "something to be done", probably because the statement starts with "I". It's very personal. "I do the thing." "I do something." But if we make a more impersonal statement, the passive form with "to be done" makes more sense:

There's nothing to be done. ~ There is nothing that can be done (by anybody) (to remedy the situation).

But note this: There's nothing to do. ~ There is nothing [interesting / suitable] for me/us to do. ~ There is nothing that I/we find [interesting / suitable] to do.

You are not going to learn this is a few hours. You'll have to see many different examples before you start to see the patterns.

CJ
Thank you so much for all your comments. And as you said, I'm not going to learn this in a few hours.

OK, well, to be more fair, I want to kind of see your agreement with other natives on internet. I am doing this solely for improving the fairness when giving an explanation.

Therefore, the following excerpts in cloze mode were gathered using yahoo. I provide hyperlinks to the articles. But, please fill the blanks first before you go and check them.
  1. "Any and all work I had to do, I did with a passion," he said. "If I have a stack of things to [...], I'm not the kind of guy to put it off." link
  2. At one point he turned and said, “There’s nothing to say and nothing to [...].” link
  3. When a high-country craving comes over me like a thunderclap, there's nothing to [...] except pack up. link
  4. Lawrence Durrell: There are only three things to [...] with a woman. You can love her, suffer for her, or turn her into literature. link
So, what's you take on them?

Actually, I was going to sum up some points about the usage of to + infinitive and to + be + verb 3, but when I came up with an idea of checking them on yahoo and found out that in some occasions they are interchangeble, I didn't know what to say since then.

Btw, I still keep as reference your explicit explanations of the implicit sentences you gave. Really some sentences with to-infinitive as modifier of noun might not be taken literally, especially by non-native speakers (like me).

Thank you in advance,

RS

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rivosuothSo, what's you take on them?
I would explain the first one as an attempt to introduce some stylistic variety into the text. There were two uses of to do in the previous two sentences, and the author may have thought it was time to vary the pattern before the text began to sound too repetitious.

The only one that surprised me was the second one. The parallel structure seems better to me: nothing to say and nothing to do.

The third emphasizes the helplessness which is characteristic of nothing to be done so that's not a very surprising usage.

The fourth might be a more subtle attempt to suggest helplessness.

This little test shows that there really is very little difference, sometimes none, between 'adjectival' to do and to be done. If there is any difference, it's that to be done can be used to focus on the helplessness that may exist within a given situation.

CJ
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